2026-01-07T12:39:14,310 Created temporary directory: /tmp/pip-ephem-wheel-cache-plhr9hpf
2026-01-07T12:39:14,312 Created temporary directory: /tmp/pip-build-tracker-d5teal5s
2026-01-07T12:39:14,313 Initialized build tracking at /tmp/pip-build-tracker-d5teal5s
2026-01-07T12:39:14,313 Created build tracker: /tmp/pip-build-tracker-d5teal5s
2026-01-07T12:39:14,314 Entered build tracker: /tmp/pip-build-tracker-d5teal5s
2026-01-07T12:39:14,315 Created temporary directory: /tmp/pip-wheel-r1y7fw27
2026-01-07T12:39:14,318 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
2026-01-07T12:39:14,320 Created temporary directory: /tmp/pip-ephem-wheel-cache-gbsivb5d
2026-01-07T12:39:14,342 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-01-07T12:39:14,346 2 location(s) to search for versions of lobster-ai:
2026-01-07T12:39:14,346 * https://pypi.org/simple/lobster-ai/
2026-01-07T12:39:14,346 * https://www.piwheels.org/simple/lobster-ai/
2026-01-07T12:39:14,346 Fetching project page and analyzing links: https://pypi.org/simple/lobster-ai/
2026-01-07T12:39:14,347 Getting page https://pypi.org/simple/lobster-ai/
2026-01-07T12:39:14,349 Found index url https://pypi.org/simple
2026-01-07T12:39:14,560 Fetched page https://pypi.org/simple/lobster-ai/ as application/vnd.pypi.simple.v1+json
2026-01-07T12:39:14,562   Skipping link: No binaries permitted for lobster-ai: https://files.pythonhosted.org/packages/25/73/1d1a25243200fd27fb678fc6ba25c4f1675657400551cb051e2f0ba608ec/lobster_ai-0.4.0.6-py3-none-any.whl (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11)
2026-01-07T12:39:14,563   Found link https://files.pythonhosted.org/packages/70/bb/d1a5b8fb3972b827f824ed05220013d162bbec24be0d8bffe790e535960b/lobster_ai-0.4.0.6.tar.gz (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11), version: 0.4.0.6
2026-01-07T12:39:14,564   Skipping link: No binaries permitted for lobster-ai: https://files.pythonhosted.org/packages/28/50/4706e55b526417192c7d0734f9300f26cbaa6f3404a258dc5e23932755d8/lobster_ai-0.4.0.7-py3-none-any.whl (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11)
2026-01-07T12:39:14,565   Found link https://files.pythonhosted.org/packages/a8/80/ed27ba2c77f7614bf149a697b450c4828da9d56fe5c8d3f0090165bf76fc/lobster_ai-0.4.0.7.tar.gz (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11), version: 0.4.0.7
2026-01-07T12:39:14,566   Skipping link: No binaries permitted for lobster-ai: https://files.pythonhosted.org/packages/d6/d8/90aa06db1b87347873b4ce21d57d45a24c7c9a7f357128242401dacf90ee/lobster_ai-0.4.0.8-py3-none-any.whl (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11)
2026-01-07T12:39:14,567   Found link https://files.pythonhosted.org/packages/69/86/8a4b462df9a8118f3de7e0685672bda6cb876c8345b4434923a5c5e941ff/lobster_ai-0.4.0.8.tar.gz (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11), version: 0.4.0.8
2026-01-07T12:39:14,567   Skipping link: No binaries permitted for lobster-ai: https://files.pythonhosted.org/packages/82/31/78340295ff44b67ccc4c5caaa6719063d7474604cd61fa9262fc35d4d956/lobster_ai-0.4.0.9-py3-none-any.whl (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11)
2026-01-07T12:39:14,568   Found link https://files.pythonhosted.org/packages/6f/e1/d7ec868a638125f79b3f450e1ecb1b9e75ed7ba1887b51849531a4b362dc/lobster_ai-0.4.0.9.tar.gz (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11), version: 0.4.0.9
2026-01-07T12:39:14,569 Fetching project page and analyzing links: https://www.piwheels.org/simple/lobster-ai/
2026-01-07T12:39:14,570 Getting page https://www.piwheels.org/simple/lobster-ai/
2026-01-07T12:39:14,571 Found index url https://www.piwheels.org/simple
2026-01-07T12:39:14,719 Fetched page https://www.piwheels.org/simple/lobster-ai/ as text/html
2026-01-07T12:39:14,722   Skipping link: No binaries permitted for lobster-ai: https://www.piwheels.org/simple/lobster-ai/lobster_ai-0.4.0.8-py3-none-any.whl#sha256=a66d81b7558824d17ab891c3a592ceb8ee53492f413d9cfdd89bdecd8fd1de85 (from https://www.piwheels.org/simple/lobster-ai/) (requires-python:>=3.11)
2026-01-07T12:39:14,722   Skipping link: No binaries permitted for lobster-ai: 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)
2026-01-07T12:39:14,723   Skipping link: No binaries permitted for lobster-ai: https://www.piwheels.org/simple/lobster-ai/lobster_ai-0.4.0.6-py3-none-any.whl#sha256=2d937b84c8a017772656d9ca05d13ea77671ba5c8b1eccb92e4129465a975502 (from https://www.piwheels.org/simple/lobster-ai/) (requires-python:>=3.11)
2026-01-07T12:39:14,723 Skipping link: not a file: https://www.piwheels.org/simple/lobster-ai/
2026-01-07T12:39:14,724 Skipping link: not a file: https://pypi.org/simple/lobster-ai/
2026-01-07T12:39:14,743 Given no hashes to check 1 links for project 'lobster-ai': discarding no candidates
2026-01-07T12:39:14,761 Collecting lobster-ai==0.4.0.9
2026-01-07T12:39:14,763   Created temporary directory: /tmp/pip-unpack-pdf243cd
2026-01-07T12:39:14,977   Downloading lobster_ai-0.4.0.9.tar.gz (1.2 MB)
2026-01-07T12:39:15,944   Added lobster-ai==0.4.0.9 from https://files.pythonhosted.org/packages/6f/e1/d7ec868a638125f79b3f450e1ecb1b9e75ed7ba1887b51849531a4b362dc/lobster_ai-0.4.0.9.tar.gz to build tracker '/tmp/pip-build-tracker-d5teal5s'
2026-01-07T12:39:15,958   Created temporary directory: /tmp/pip-build-env-r3fad61v
2026-01-07T12:39:15,964   Installing build dependencies: started
2026-01-07T12:39:15,966   Running command pip subprocess to install build dependencies
2026-01-07T12:39:17,118   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-01-07T12:39:17,776   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
2026-01-07T12:39:17,800   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-01-07T12:39:19,761   Collecting setuptools>=65.0
2026-01-07T12:39:19,863     Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB)
2026-01-07T12:39:20,149   Collecting wheel
2026-01-07T12:39:20,166     Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB)
2026-01-07T12:39:23,144   Installing collected packages: wheel, setuptools
2026-01-07T12:39:23,389     Creating /tmp/pip-build-env-r3fad61v/overlay/local/bin
2026-01-07T12:39:23,391     changing mode of /tmp/pip-build-env-r3fad61v/overlay/local/bin/wheel to 755
2026-01-07T12:39:27,082   Successfully installed setuptools-80.9.0 wheel-0.45.1
2026-01-07T12:39:27,357   Installing build dependencies: finished with status 'done'
2026-01-07T12:39:27,363   Getting requirements to build wheel: started
2026-01-07T12:39:27,364   Running command Getting requirements to build wheel
2026-01-07T12:39:28,043   /tmp/pip-build-env-r3fad61v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml`
2026-01-07T12:39:28,043     corresp(dist, value, root_dir)
2026-01-07T12:39:28,044   /tmp/pip-build-env-r3fad61v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2026-01-07T12:39:28,045     corresp(dist, value, root_dir)
2026-01-07T12:39:28,046   /tmp/pip-build-env-r3fad61v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies)
2026-01-07T12:39:28,046     corresp(dist, value, root_dir)
2026-01-07T12:39:28,154   running egg_info
2026-01-07T12:39:28,161   writing lobster_ai.egg-info/PKG-INFO
2026-01-07T12:39:28,191   writing dependency_links to lobster_ai.egg-info/dependency_links.txt
2026-01-07T12:39:28,193   writing entry points to lobster_ai.egg-info/entry_points.txt
2026-01-07T12:39:28,213   writing requirements to lobster_ai.egg-info/requires.txt
2026-01-07T12:39:28,214   writing top-level names to lobster_ai.egg-info/top_level.txt
2026-01-07T12:39:28,360   reading manifest file 'lobster_ai.egg-info/SOURCES.txt'
2026-01-07T12:39:28,376   adding license file 'LICENSE'
2026-01-07T12:39:28,391   writing manifest file 'lobster_ai.egg-info/SOURCES.txt'
2026-01-07T12:39:28,490   Getting requirements to build wheel: finished with status 'done'
2026-01-07T12:39:28,494   Created temporary directory: /tmp/pip-modern-metadata-ic91gbnf
2026-01-07T12:39:28,496   Preparing metadata (pyproject.toml): started
2026-01-07T12:39:28,497   Running command Preparing metadata (pyproject.toml)
2026-01-07T12:39:29,132   /tmp/pip-build-env-r3fad61v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml`
2026-01-07T12:39:29,132     corresp(dist, value, root_dir)
2026-01-07T12:39:29,132   /tmp/pip-build-env-r3fad61v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2026-01-07T12:39:29,133     corresp(dist, value, root_dir)
2026-01-07T12:39:29,134   /tmp/pip-build-env-r3fad61v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies)
2026-01-07T12:39:29,134     corresp(dist, value, root_dir)
2026-01-07T12:39:29,237   running dist_info
2026-01-07T12:39:29,250   creating /tmp/pip-modern-metadata-ic91gbnf/lobster_ai.egg-info
2026-01-07T12:39:29,250   writing /tmp/pip-modern-metadata-ic91gbnf/lobster_ai.egg-info/PKG-INFO
2026-01-07T12:39:29,281   writing dependency_links to /tmp/pip-modern-metadata-ic91gbnf/lobster_ai.egg-info/dependency_links.txt
2026-01-07T12:39:29,283   writing entry points to /tmp/pip-modern-metadata-ic91gbnf/lobster_ai.egg-info/entry_points.txt
2026-01-07T12:39:29,302   writing requirements to /tmp/pip-modern-metadata-ic91gbnf/lobster_ai.egg-info/requires.txt
2026-01-07T12:39:29,304   writing top-level names to /tmp/pip-modern-metadata-ic91gbnf/lobster_ai.egg-info/top_level.txt
2026-01-07T12:39:29,305   writing manifest file '/tmp/pip-modern-metadata-ic91gbnf/lobster_ai.egg-info/SOURCES.txt'
2026-01-07T12:39:29,442   reading manifest file '/tmp/pip-modern-metadata-ic91gbnf/lobster_ai.egg-info/SOURCES.txt'
2026-01-07T12:39:29,444   adding license file 'LICENSE'
2026-01-07T12:39:29,455   writing manifest file '/tmp/pip-modern-metadata-ic91gbnf/lobster_ai.egg-info/SOURCES.txt'
2026-01-07T12:39:29,457   creating '/tmp/pip-modern-metadata-ic91gbnf/lobster_ai-0.4.0.9.dist-info'
2026-01-07T12:39:29,587   Preparing metadata (pyproject.toml): finished with status 'done'
2026-01-07T12:39:29,595   Source in /tmp/pip-wheel-r1y7fw27/lobster-ai_c2211d964ae14c62a7d42dc1827634ce has version 0.4.0.9, which satisfies requirement lobster-ai==0.4.0.9 from https://files.pythonhosted.org/packages/6f/e1/d7ec868a638125f79b3f450e1ecb1b9e75ed7ba1887b51849531a4b362dc/lobster_ai-0.4.0.9.tar.gz
2026-01-07T12:39:29,596   Removed lobster-ai==0.4.0.9 from https://files.pythonhosted.org/packages/6f/e1/d7ec868a638125f79b3f450e1ecb1b9e75ed7ba1887b51849531a4b362dc/lobster_ai-0.4.0.9.tar.gz from build tracker '/tmp/pip-build-tracker-d5teal5s'
2026-01-07T12:39:29,608 Created temporary directory: /tmp/pip-unpack-wrurrk4g
2026-01-07T12:39:29,609 Building wheels for collected packages: lobster-ai
2026-01-07T12:39:29,613   Created temporary directory: /tmp/pip-wheel-_u005opw
2026-01-07T12:39:29,613   Destination directory: /tmp/pip-wheel-_u005opw
2026-01-07T12:39:29,616   Building wheel for lobster-ai (pyproject.toml): started
2026-01-07T12:39:29,617   Running command Building wheel for lobster-ai (pyproject.toml)
2026-01-07T12:39:30,226   /tmp/pip-build-env-r3fad61v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml`
2026-01-07T12:39:30,226     corresp(dist, value, root_dir)
2026-01-07T12:39:30,227   /tmp/pip-build-env-r3fad61v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2026-01-07T12:39:30,227     corresp(dist, value, root_dir)
2026-01-07T12:39:30,228   /tmp/pip-build-env-r3fad61v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies)
2026-01-07T12:39:30,228     corresp(dist, value, root_dir)
2026-01-07T12:39:30,320   running bdist_wheel
2026-01-07T12:39:30,341   running build
2026-01-07T12:39:30,341   running build_py
2026-01-07T12:39:30,348   creating build/lib/lobster
2026-01-07T12:39:30,351   copying lobster/version.py -> build/lib/lobster
2026-01-07T12:39:30,353   copying lobster/__main__.py -> build/lib/lobster
2026-01-07T12:39:30,355   copying lobster/main.py -> build/lib/lobster
2026-01-07T12:39:30,357   copying lobster/cli.py -> build/lib/lobster
2026-01-07T12:39:30,368   copying lobster/_version.py -> build/lib/lobster
2026-01-07T12:39:30,370   creating build/lib/lobster/lobster_cloud
2026-01-07T12:39:30,371   copying lobster/lobster_cloud/__init__.py -> build/lib/lobster/lobster_cloud
2026-01-07T12:39:30,374   copying lobster/lobster_cloud/client.py -> build/lib/lobster/lobster_cloud
2026-01-07T12:39:30,378   creating build/lib/lobster/agents
2026-01-07T12:39:30,379   copying lobster/agents/supervisor.py -> build/lib/lobster/agents
2026-01-07T12:39:30,382   copying lobster/agents/__init__.py -> build/lib/lobster/agents
2026-01-07T12:39:30,383   copying lobster/agents/draw_graph.py -> build/lib/lobster/agents
2026-01-07T12:39:30,385   copying lobster/agents/visualization_expert.py -> build/lib/lobster/agents
2026-01-07T12:39:30,388   copying lobster/agents/research_agent.py -> build/lib/lobster/agents
2026-01-07T12:39:30,393   copying lobster/agents/state.py -> build/lib/lobster/agents
2026-01-07T12:39:30,395   copying lobster/agents/data_expert.py -> build/lib/lobster/agents
2026-01-07T12:39:30,399   copying lobster/agents/graph.py -> build/lib/lobster/agents
2026-01-07T12:39:30,401   copying lobster/agents/data_expert_assistant.py -> build/lib/lobster/agents
2026-01-07T12:39:30,407   creating build/lib/lobster/core
2026-01-07T12:39:30,408   copying lobster/core/component_registry.py -> build/lib/lobster/core
2026-01-07T12:39:30,410   copying lobster/core/download_queue.py -> build/lib/lobster/core
2026-01-07T12:39:30,414   copying lobster/core/notebook_validator.py -> build/lib/lobster/core
2026-01-07T12:39:30,417   copying lobster/core/plot_manager.py -> build/lib/lobster/core
2026-01-07T12:39:30,420   copying lobster/core/notebook_exporter.py -> build/lib/lobster/core
2026-01-07T12:39:30,423   copying lobster/core/__init__.py -> build/lib/lobster/core
2026-01-07T12:39:30,425   copying lobster/core/archive_utils.py -> build/lib/lobster/core
2026-01-07T12:39:30,428   copying lobster/core/publication_queue.py -> build/lib/lobster/core
2026-01-07T12:39:30,430   copying lobster/core/ris_parser.py -> build/lib/lobster/core
2026-01-07T12:39:30,433   copying lobster/core/notebook_executor.py -> build/lib/lobster/core
2026-01-07T12:39:30,436   copying lobster/core/provenance.py -> build/lib/lobster/core
2026-01-07T12:39:30,439   copying lobster/core/config_resolver.py -> build/lib/lobster/core
2026-01-07T12:39:30,441   copying lobster/core/workspace.py -> build/lib/lobster/core
2026-01-07T12:39:30,443   copying lobster/core/client.py -> build/lib/lobster/core
2026-01-07T12:39:30,447   copying lobster/core/license_manager.py -> build/lib/lobster/core
2026-01-07T12:39:30,450   copying lobster/core/exceptions.py -> build/lib/lobster/core
2026-01-07T12:39:30,452   copying lobster/core/data_manager_v2.py -> build/lib/lobster/core
2026-01-07T12:39:30,458   copying lobster/core/plugin_loader.py -> build/lib/lobster/core
2026-01-07T12:39:30,460   copying lobster/core/queue_storage.py -> build/lib/lobster/core
2026-01-07T12:39:30,462   copying lobster/core/ir_coverage.py -> build/lib/lobster/core
2026-01-07T12:39:30,465   copying lobster/core/analysis_ir.py -> build/lib/lobster/core
2026-01-07T12:39:30,468   creating build/lib/lobster/tools
2026-01-07T12:39:30,470   copying lobster/tools/gpu_detector.py -> build/lib/lobster/tools
2026-01-07T12:39:30,472   copying lobster/tools/geo_parser.py -> build/lib/lobster/tools
2026-01-07T12:39:30,474   copying lobster/tools/custom_code_tool.py -> build/lib/lobster/tools
2026-01-07T12:39:30,476   copying lobster/tools/__init__.py -> build/lib/lobster/tools
2026-01-07T12:39:30,478   copying lobster/tools/enhanced_handoff_tool.py -> build/lib/lobster/tools
2026-01-07T12:39:30,481   copying lobster/tools/expert_handoff_patterns.py -> build/lib/lobster/tools
2026-01-07T12:39:30,484   copying lobster/tools/workspace_tool.py -> build/lib/lobster/tools
2026-01-07T12:39:30,488   copying lobster/tools/todo_tools.py -> build/lib/lobster/tools
2026-01-07T12:39:30,491   copying lobster/tools/workflow_tracker.py -> build/lib/lobster/tools
2026-01-07T12:39:30,493   copying lobster/tools/rate_limiter.py -> build/lib/lobster/tools
2026-01-07T12:39:30,497   copying lobster/tools/geo_downloader.py -> build/lib/lobster/tools
2026-01-07T12:39:30,499   copying lobster/tools/pipeline_strategy.py -> build/lib/lobster/tools
2026-01-07T12:39:30,501   copying lobster/tools/url_transforms.py -> build/lib/lobster/tools
2026-01-07T12:39:30,503   copying lobster/tools/handoff_tool.py -> build/lib/lobster/tools
2026-01-07T12:39:30,505   copying lobster/tools/download_orchestrator.py -> build/lib/lobster/tools
2026-01-07T12:39:30,507   copying lobster/tools/expert_handoff_manager.py -> build/lib/lobster/tools
2026-01-07T12:39:30,510   creating build/lib/lobster/ui
2026-01-07T12:39:30,512   copying lobster/ui/console_manager.py -> build/lib/lobster/ui
2026-01-07T12:39:30,514   copying lobster/ui/__init__.py -> build/lib/lobster/ui
2026-01-07T12:39:30,516   copying lobster/ui/commands.py -> build/lib/lobster/ui
2026-01-07T12:39:30,519   copying lobster/ui/progress_manager.py -> build/lib/lobster/ui
2026-01-07T12:39:30,522   copying lobster/ui/themes.py -> build/lib/lobster/ui
2026-01-07T12:39:30,524   copying lobster/ui/live_dashboard.py -> build/lib/lobster/ui
2026-01-07T12:39:30,527   copying lobster/ui/os_app.py -> build/lib/lobster/ui
2026-01-07T12:39:30,529   creating build/lib/lobster/config
2026-01-07T12:39:30,530   copying lobster/config/llm_factory.py -> build/lib/lobster/config
2026-01-07T12:39:30,533   copying lobster/config/agent_capabilities.py -> build/lib/lobster/config
2026-01-07T12:39:30,536   copying lobster/config/__init__.py -> build/lib/lobster/config
2026-01-07T12:39:30,538   copying lobster/config/subscription_tiers.py -> build/lib/lobster/config
2026-01-07T12:39:30,540   copying lobster/config/workspace_config.py -> build/lib/lobster/config
2026-01-07T12:39:30,542   copying lobster/config/base_config.py -> build/lib/lobster/config
2026-01-07T12:39:30,544   copying lobster/config/constants.py -> build/lib/lobster/config
2026-01-07T12:39:30,546   copying lobster/config/config_manager.py -> build/lib/lobster/config
2026-01-07T12:39:30,549   copying lobster/config/agent_config.py -> build/lib/lobster/config
2026-01-07T12:39:30,552   copying lobster/config/global_config.py -> build/lib/lobster/config
2026-01-07T12:39:30,554   copying lobster/config/model_service.py -> build/lib/lobster/config
2026-01-07T12:39:30,557   copying lobster/config/ollama_service.py -> build/lib/lobster/config
2026-01-07T12:39:30,559   copying lobster/config/supervisor_config.py -> build/lib/lobster/config
2026-01-07T12:39:30,562   copying lobster/config/settings.py -> build/lib/lobster/config
2026-01-07T12:39:30,564   copying lobster/config/provider_setup.py -> build/lib/lobster/config
2026-01-07T12:39:30,567   copying lobster/config/agent_registry.py -> build/lib/lobster/config
2026-01-07T12:39:30,569   creating build/lib/lobster/services
2026-01-07T12:39:30,570   copying lobster/services/__init__.py -> build/lib/lobster/services
2026-01-07T12:39:30,573   creating build/lib/lobster/cli_internal
2026-01-07T12:39:30,574   copying lobster/cli_internal/__init__.py -> build/lib/lobster/cli_internal
2026-01-07T12:39:30,576   creating build/lib/lobster/utils
2026-01-07T12:39:30,577   copying lobster/utils/__init__.py -> build/lib/lobster/utils
2026-01-07T12:39:30,579   copying lobster/utils/deviance.py -> build/lib/lobster/utils
2026-01-07T12:39:30,581   copying lobster/utils/error_handlers.py -> build/lib/lobster/utils
2026-01-07T12:39:30,584   copying lobster/utils/file_analyzer.py -> build/lib/lobster/utils
2026-01-07T12:39:30,586   copying lobster/utils/json_extractor.py -> build/lib/lobster/utils
2026-01-07T12:39:30,589   copying lobster/utils/logger.py -> build/lib/lobster/utils
2026-01-07T12:39:30,591   copying lobster/utils/callbacks.py -> build/lib/lobster/utils
2026-01-07T12:39:30,593   copying lobster/utils/progress_wrapper.py -> build/lib/lobster/utils
2026-01-07T12:39:30,596   copying lobster/utils/ssl_utils.py -> build/lib/lobster/utils
2026-01-07T12:39:30,598   copying lobster/utils/system.py -> build/lib/lobster/utils
2026-01-07T12:39:30,600   copying lobster/utils/file_naming.py -> build/lib/lobster/utils
2026-01-07T12:39:30,603   creating build/lib/lobster/agents/archive
2026-01-07T12:39:30,604   copying lobster/agents/archive/research_agent_assistant.py -> build/lib/lobster/agents/archive
2026-01-07T12:39:30,607   creating build/lib/lobster/agents/proteomics
2026-01-07T12:39:30,608   copying lobster/agents/proteomics/__init__.py -> build/lib/lobster/agents/proteomics
2026-01-07T12:39:30,610   copying lobster/agents/proteomics/state.py -> build/lib/lobster/agents/proteomics
2026-01-07T12:39:30,613   creating build/lib/lobster/agents/transcriptomics
2026-01-07T12:39:30,614   copying lobster/agents/transcriptomics/transcriptomics_expert.py -> build/lib/lobster/agents/transcriptomics
2026-01-07T12:39:30,617   copying lobster/agents/transcriptomics/__init__.py -> build/lib/lobster/agents/transcriptomics
2026-01-07T12:39:30,619   copying lobster/agents/transcriptomics/shared_tools.py -> build/lib/lobster/agents/transcriptomics
2026-01-07T12:39:30,622   copying lobster/agents/transcriptomics/de_analysis_expert.py -> build/lib/lobster/agents/transcriptomics
2026-01-07T12:39:30,626   copying lobster/agents/transcriptomics/state.py -> build/lib/lobster/agents/transcriptomics
2026-01-07T12:39:30,628   copying lobster/agents/transcriptomics/annotation_expert.py -> build/lib/lobster/agents/transcriptomics
2026-01-07T12:39:30,632   creating build/lib/lobster/agents/langgraph_supervisor
2026-01-07T12:39:30,633   copying lobster/agents/langgraph_supervisor/supervisor.py -> build/lib/lobster/agents/langgraph_supervisor
2026-01-07T12:39:30,636   copying lobster/agents/langgraph_supervisor/agent_name.py -> build/lib/lobster/agents/langgraph_supervisor
2026-01-07T12:39:30,638   copying lobster/agents/langgraph_supervisor/__init__.py -> build/lib/lobster/agents/langgraph_supervisor
2026-01-07T12:39:30,640   copying lobster/agents/langgraph_supervisor/handoff.py -> build/lib/lobster/agents/langgraph_supervisor
2026-01-07T12:39:30,643   creating build/lib/lobster/core/backends
2026-01-07T12:39:30,644   copying lobster/core/backends/base.py -> build/lib/lobster/core/backends
2026-01-07T12:39:30,646   copying lobster/core/backends/__init__.py -> build/lib/lobster/core/backends
2026-01-07T12:39:30,648   copying lobster/core/backends/h5ad_backend.py -> build/lib/lobster/core/backends
2026-01-07T12:39:30,652   copying lobster/core/backends/mudata_backend.py -> build/lib/lobster/core/backends
2026-01-07T12:39:30,655   creating build/lib/lobster/core/interfaces
2026-01-07T12:39:30,656   copying lobster/core/interfaces/base_client.py -> build/lib/lobster/core/interfaces
2026-01-07T12:39:30,658   copying lobster/core/interfaces/download_service.py -> build/lib/lobster/core/interfaces
2026-01-07T12:39:30,661   copying lobster/core/interfaces/__init__.py -> build/lib/lobster/core/interfaces
2026-01-07T12:39:30,663   copying lobster/core/interfaces/adapter.py -> build/lib/lobster/core/interfaces
2026-01-07T12:39:30,665   copying lobster/core/interfaces/backend.py -> build/lib/lobster/core/interfaces
2026-01-07T12:39:30,668   copying lobster/core/interfaces/validator.py -> build/lib/lobster/core/interfaces
2026-01-07T12:39:30,671   creating build/lib/lobster/core/adapters
2026-01-07T12:39:30,672   copying lobster/core/adapters/base.py -> build/lib/lobster/core/adapters
2026-01-07T12:39:30,674   copying lobster/core/adapters/__init__.py -> build/lib/lobster/core/adapters
2026-01-07T12:39:30,676   copying lobster/core/adapters/transcriptomics_adapter.py -> build/lib/lobster/core/adapters
2026-01-07T12:39:30,679   copying lobster/core/adapters/pseudobulk_adapter.py -> build/lib/lobster/core/adapters
2026-01-07T12:39:30,681   copying lobster/core/adapters/proteomics_adapter.py -> build/lib/lobster/core/adapters
2026-01-07T12:39:30,684   copying lobster/core/adapters/protein_structure_adapter.py -> build/lib/lobster/core/adapters
2026-01-07T12:39:30,687   creating build/lib/lobster/core/utils
2026-01-07T12:39:30,688   copying lobster/core/utils/__init__.py -> build/lib/lobster/core/utils
2026-01-07T12:39:30,690   copying lobster/core/utils/h5ad_utils.py -> build/lib/lobster/core/utils
2026-01-07T12:39:30,693   creating build/lib/lobster/core/identifiers
2026-01-07T12:39:30,694   copying lobster/core/identifiers/accession_resolver.py -> build/lib/lobster/core/identifiers
2026-01-07T12:39:30,697   copying lobster/core/identifiers/__init__.py -> build/lib/lobster/core/identifiers
2026-01-07T12:39:30,700   creating build/lib/lobster/core/schemas
2026-01-07T12:39:30,701   copying lobster/core/schemas/transcriptomics.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,704   copying lobster/core/schemas/download_queue.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,707   copying lobster/core/schemas/validation.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,710   copying lobster/core/schemas/database_registry.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,712   copying lobster/core/schemas/metabolomics.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,715   copying lobster/core/schemas/__init__.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,717   copying lobster/core/schemas/sra.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,719   copying lobster/core/schemas/publication_queue.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,722   copying lobster/core/schemas/proteomics.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,725   copying lobster/core/schemas/metagenomics.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,728   copying lobster/core/schemas/download_urls.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,731   copying lobster/core/schemas/export_schemas.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,733   copying lobster/core/schemas/database_mappings.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,736   copying lobster/core/schemas/protein_structure.py -> build/lib/lobster/core/schemas
2026-01-07T12:39:30,739   creating build/lib/lobster/tools/archive
2026-01-07T12:39:30,740   copying lobster/tools/archive/unified_content_service.py -> build/lib/lobster/tools/archive
2026-01-07T12:39:30,744   copying lobster/tools/archive/publication_service.py -> build/lib/lobster/tools/archive
2026-01-07T12:39:30,747   creating build/lib/lobster/tools/providers
2026-01-07T12:39:30,748   copying lobster/tools/providers/base_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,751   copying lobster/tools/providers/publication_resolver.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,754   copying lobster/tools/providers/__init__.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,756   copying lobster/tools/providers/webpage_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,759   copying lobster/tools/providers/pride_normalizer.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,762   copying lobster/tools/providers/geo_utils.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,764   copying lobster/tools/providers/biorxiv_medrxiv_config.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,766   copying lobster/tools/providers/pubmed_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,770   copying lobster/tools/providers/pdb_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,772   copying lobster/tools/providers/pmc_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,776   copying lobster/tools/providers/organism_enum.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,778   copying lobster/tools/providers/structure_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,780   copying lobster/tools/providers/sra_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,784   copying lobster/tools/providers/abstract_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,786   copying lobster/tools/providers/biopython_entrez_wrapper.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,788   copying lobster/tools/providers/massive_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,791   copying lobster/tools/providers/geo_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,795   copying lobster/tools/providers/provider_registry.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,797   copying lobster/tools/providers/biorxiv_medrxiv_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,800   copying lobster/tools/providers/pride_provider.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,803   copying lobster/tools/providers/ncbi_query_builder.py -> build/lib/lobster/tools/providers
2026-01-07T12:39:30,807   creating build/lib/lobster/ui/callbacks
2026-01-07T12:39:30,808   copying lobster/ui/callbacks/__init__.py -> build/lib/lobster/ui/callbacks
2026-01-07T12:39:30,810   copying lobster/ui/callbacks/textual_callback.py -> build/lib/lobster/ui/callbacks
2026-01-07T12:39:30,813   creating build/lib/lobster/ui/components
2026-01-07T12:39:30,814   copying lobster/ui/components/__init__.py -> build/lib/lobster/ui/components
2026-01-07T12:39:30,816   copying lobster/ui/components/parallel_workers_progress.py -> build/lib/lobster/ui/components
2026-01-07T12:39:30,819   copying lobster/ui/components/multi_progress.py -> build/lib/lobster/ui/components
2026-01-07T12:39:30,821   copying lobster/ui/components/status_display.py -> build/lib/lobster/ui/components
2026-01-07T12:39:30,824   copying lobster/ui/components/file_tree.py -> build/lib/lobster/ui/components
2026-01-07T12:39:30,827   creating build/lib/lobster/ui/formatters
2026-01-07T12:39:30,828   copying lobster/ui/formatters/__init__.py -> build/lib/lobster/ui/formatters
2026-01-07T12:39:30,830   creating build/lib/lobster/ui/screens
2026-01-07T12:39:30,831   copying lobster/ui/screens/analysis_screen.py -> build/lib/lobster/ui/screens
2026-01-07T12:39:30,834   copying lobster/ui/screens/__init__.py -> build/lib/lobster/ui/screens
2026-01-07T12:39:30,836   creating build/lib/lobster/ui/services
2026-01-07T12:39:30,838   copying lobster/ui/services/__init__.py -> build/lib/lobster/ui/services
2026-01-07T12:39:30,840   copying lobster/ui/services/error_service.py -> build/lib/lobster/ui/services
2026-01-07T12:39:30,843   creating build/lib/lobster/ui/widgets
2026-01-07T12:39:30,844   copying lobster/ui/widgets/results_display.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,846   copying lobster/ui/widgets/__init__.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,848   copying lobster/ui/widgets/queue_panel.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,850   copying lobster/ui/widgets/data_hub.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,853   copying lobster/ui/widgets/status_bar.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,855   copying lobster/ui/widgets/connections_panel.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,857   copying lobster/ui/widgets/plot_preview.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,859   copying lobster/ui/widgets/activity_log.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,861   copying lobster/ui/widgets/modality_list.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,863   copying lobster/ui/widgets/agents_panel.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,866   copying lobster/ui/widgets/chat_message.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,868   copying lobster/ui/widgets/query_prompt.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,870   copying lobster/ui/widgets/system_info.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,872   copying lobster/ui/widgets/token_usage_panel.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,874   copying lobster/ui/widgets/queue_status_bar.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,876   copying lobster/ui/widgets/error_modal.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,879   copying lobster/ui/widgets/adapters_panel.py -> build/lib/lobster/ui/widgets
2026-01-07T12:39:30,882   creating build/lib/lobster/config/providers
2026-01-07T12:39:30,883   copying lobster/config/providers/base_provider.py -> build/lib/lobster/config/providers
2026-01-07T12:39:30,885   copying lobster/config/providers/__init__.py -> build/lib/lobster/config/providers
2026-01-07T12:39:30,887   copying lobster/config/providers/gemini_provider.py -> build/lib/lobster/config/providers
2026-01-07T12:39:30,889   copying lobster/config/providers/registry.py -> build/lib/lobster/config/providers
2026-01-07T12:39:30,891   copying lobster/config/providers/anthropic_provider.py -> build/lib/lobster/config/providers
2026-01-07T12:39:30,893   copying lobster/config/providers/ollama_provider.py -> build/lib/lobster/config/providers
2026-01-07T12:39:30,896   copying lobster/config/providers/bedrock_provider.py -> build/lib/lobster/config/providers
2026-01-07T12:39:30,898   creating build/lib/lobster/services/analysis
2026-01-07T12:39:30,899   copying lobster/services/analysis/__init__.py -> build/lib/lobster/services/analysis
2026-01-07T12:39:30,901   copying lobster/services/analysis/differential_formula_service.py -> build/lib/lobster/services/analysis
2026-01-07T12:39:30,904   copying lobster/services/analysis/bulk_rnaseq_service.py -> build/lib/lobster/services/analysis
2026-01-07T12:39:30,908   copying lobster/services/analysis/enhanced_singlecell_service.py -> build/lib/lobster/services/analysis
2026-01-07T12:39:30,911   copying lobster/services/analysis/pseudobulk_service.py -> build/lib/lobster/services/analysis
2026-01-07T12:39:30,914   copying lobster/services/analysis/scvi_embedding_service.py -> build/lib/lobster/services/analysis
2026-01-07T12:39:30,917   copying lobster/services/analysis/clustering_service.py -> build/lib/lobster/services/analysis
2026-01-07T12:39:30,921   copying lobster/services/analysis/structure_analysis_service.py -> build/lib/lobster/services/analysis
2026-01-07T12:39:30,925   creating build/lib/lobster/services/data_access
2026-01-07T12:39:30,926   copying lobster/services/data_access/geo_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,934   copying lobster/services/data_access/workspace_content_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,938   copying lobster/services/data_access/pride_download_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,940   copying lobster/services/data_access/docling_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,944   copying lobster/services/data_access/__init__.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,946   copying lobster/services/data_access/protein_structure_fetch_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,948   copying lobster/services/data_access/geo_fallback_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,951   copying lobster/services/data_access/geo_download_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,954   copying lobster/services/data_access/content_access_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,957   copying lobster/services/data_access/sra_download_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,960   copying lobster/services/data_access/massive_download_service.py -> build/lib/lobster/services/data_access
2026-01-07T12:39:30,963   creating build/lib/lobster/services/quality
2026-01-07T12:39:30,964   copying lobster/services/quality/__init__.py -> build/lib/lobster/services/quality
2026-01-07T12:39:30,966   copying lobster/services/quality/preprocessing_service.py -> build/lib/lobster/services/quality
2026-01-07T12:39:30,969   copying lobster/services/quality/quality_service.py -> build/lib/lobster/services/quality
2026-01-07T12:39:30,972   creating build/lib/lobster/services/orchestration
2026-01-07T12:39:30,973   copying lobster/services/orchestration/__init__.py -> build/lib/lobster/services/orchestration
2026-01-07T12:39:30,975   copying lobster/services/orchestration/publication_processing_service.py -> build/lib/lobster/services/orchestration
2026-01-07T12:39:30,979   creating build/lib/lobster/services/execution
2026-01-07T12:39:30,980   copying lobster/services/execution/execution_context_builder.py -> build/lib/lobster/services/execution
2026-01-07T12:39:30,983   copying lobster/services/execution/__init__.py -> build/lib/lobster/services/execution
2026-01-07T12:39:30,985   copying lobster/services/execution/custom_code_execution_service.py -> build/lib/lobster/services/execution
2026-01-07T12:39:30,988   creating build/lib/lobster/services/visualization
2026-01-07T12:39:30,989   copying lobster/services/visualization/__init__.py -> build/lib/lobster/services/visualization
2026-01-07T12:39:30,991   copying lobster/services/visualization/pymol_visualization_service.py -> build/lib/lobster/services/visualization
2026-01-07T12:39:30,994   copying lobster/services/visualization/bulk_visualization_service.py -> build/lib/lobster/services/visualization
2026-01-07T12:39:30,997   copying lobster/services/visualization/visualization_service.py -> build/lib/lobster/services/visualization
2026-01-07T12:39:31,001   creating build/lib/lobster/services/templates
2026-01-07T12:39:31,002   copying lobster/services/templates/__init__.py -> build/lib/lobster/services/templates
2026-01-07T12:39:31,004   copying lobster/services/templates/annotation_templates.py -> build/lib/lobster/services/templates
2026-01-07T12:39:31,009   creating build/lib/lobster/services/data_management
2026-01-07T12:39:31,010   copying lobster/services/data_management/__init__.py -> build/lib/lobster/services/data_management
2026-01-07T12:39:31,012   copying lobster/services/data_management/concatenation_service.py -> build/lib/lobster/services/data_management
2026-01-07T12:39:31,016   copying lobster/services/data_management/modality_management_service.py -> build/lib/lobster/services/data_management
2026-01-07T12:39:31,019   creating build/lib/lobster/services/metadata
2026-01-07T12:39:31,021   copying lobster/services/metadata/__init__.py -> build/lib/lobster/services/metadata
2026-01-07T12:39:31,023   copying lobster/services/metadata/metadata_validation_service.py -> build/lib/lobster/services/metadata
2026-01-07T12:39:31,026   copying lobster/services/metadata/identifier_provenance_service.py -> build/lib/lobster/services/metadata
2026-01-07T12:39:31,029   copying lobster/services/metadata/metadata_standardization_service.py -> build/lib/lobster/services/metadata
2026-01-07T12:39:31,032   copying lobster/services/metadata/manual_annotation_service.py -> build/lib/lobster/services/metadata
2026-01-07T12:39:31,036   copying lobster/services/metadata/sample_grouping_service.py -> build/lib/lobster/services/metadata
2026-01-07T12:39:31,039   creating build/lib/lobster/services/ml
2026-01-07T12:39:31,041   copying lobster/services/ml/__init__.py -> build/lib/lobster/services/ml
2026-01-07T12:39:31,044   creating build/lib/lobster/services/data_access/geo
2026-01-07T12:39:31,045   copying lobster/services/data_access/geo/strategy.py -> build/lib/lobster/services/data_access/geo
2026-01-07T12:39:31,048   copying lobster/services/data_access/geo/parser.py -> build/lib/lobster/services/data_access/geo
2026-01-07T12:39:31,053   copying lobster/services/data_access/geo/__init__.py -> build/lib/lobster/services/data_access/geo
2026-01-07T12:39:31,055   copying lobster/services/data_access/geo/constants.py -> build/lib/lobster/services/data_access/geo
2026-01-07T12:39:31,058   copying lobster/services/data_access/geo/facade.py -> build/lib/lobster/services/data_access/geo
2026-01-07T12:39:31,060   copying lobster/services/data_access/geo/downloader.py -> build/lib/lobster/services/data_access/geo
2026-01-07T12:39:31,064   creating build/lib/lobster/services/data_access/geo/loaders
2026-01-07T12:39:31,066   copying lobster/services/data_access/geo/loaders/__init__.py -> build/lib/lobster/services/data_access/geo/loaders
2026-01-07T12:39:31,068   copying lobster/services/data_access/geo/loaders/tenx.py -> build/lib/lobster/services/data_access/geo/loaders
2026-01-07T12:39:31,071   creating build/lib/lobster/services/data_access/geo/metadata
2026-01-07T12:39:31,073   copying lobster/services/data_access/geo/metadata/__init__.py -> build/lib/lobster/services/data_access/geo/metadata
2026-01-07T12:39:31,076   creating build/lib/lobster/services/data_access/geo/sample
2026-01-07T12:39:31,077   copying lobster/services/data_access/geo/sample/__init__.py -> build/lib/lobster/services/data_access/geo/sample
2026-01-07T12:39:31,080   creating build/lib/lobster/services/data_access/geo/utils
2026-01-07T12:39:31,081   copying lobster/services/data_access/geo/utils/__init__.py -> build/lib/lobster/services/data_access/geo/utils
2026-01-07T12:39:31,084   creating build/lib/lobster/services/metadata/protocol_extraction
2026-01-07T12:39:31,086   copying lobster/services/metadata/protocol_extraction/base.py -> build/lib/lobster/services/metadata/protocol_extraction
2026-01-07T12:39:31,089   copying lobster/services/metadata/protocol_extraction/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction
2026-01-07T12:39:31,093   creating build/lib/lobster/services/metadata/protocol_extraction/mass_spec
2026-01-07T12:39:31,094   copying lobster/services/metadata/protocol_extraction/mass_spec/service.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec
2026-01-07T12:39:31,098   copying lobster/services/metadata/protocol_extraction/mass_spec/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec
2026-01-07T12:39:31,101   copying lobster/services/metadata/protocol_extraction/mass_spec/details.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec
2026-01-07T12:39:31,104   creating build/lib/lobster/services/metadata/protocol_extraction/amplicon
2026-01-07T12:39:31,106   copying lobster/services/metadata/protocol_extraction/amplicon/service.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon
2026-01-07T12:39:31,111   copying lobster/services/metadata/protocol_extraction/amplicon/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon
2026-01-07T12:39:31,114   copying lobster/services/metadata/protocol_extraction/amplicon/details.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon
2026-01-07T12:39:31,118   creating build/lib/lobster/services/metadata/protocol_extraction/rnaseq
2026-01-07T12:39:31,119   copying lobster/services/metadata/protocol_extraction/rnaseq/service.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq
2026-01-07T12:39:31,123   copying lobster/services/metadata/protocol_extraction/rnaseq/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq
2026-01-07T12:39:31,126   copying lobster/services/metadata/protocol_extraction/rnaseq/details.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq
2026-01-07T12:39:31,130   creating build/lib/lobster/cli_internal/utils
2026-01-07T12:39:31,131   copying lobster/cli_internal/utils/__init__.py -> build/lib/lobster/cli_internal/utils
2026-01-07T12:39:31,134   copying lobster/cli_internal/utils/path_resolution.py -> build/lib/lobster/cli_internal/utils
2026-01-07T12:39:31,138   creating build/lib/lobster/cli_internal/commands
2026-01-07T12:39:31,140   copying lobster/cli_internal/commands/__init__.py -> build/lib/lobster/cli_internal/commands
2026-01-07T12:39:31,143   copying lobster/cli_internal/commands/output_adapter.py -> build/lib/lobster/cli_internal/commands
2026-01-07T12:39:31,146   creating build/lib/lobster/cli_internal/commands/light
2026-01-07T12:39:31,148   copying lobster/cli_internal/commands/light/queue_commands.py -> build/lib/lobster/cli_internal/commands/light
2026-01-07T12:39:31,151   copying lobster/cli_internal/commands/light/__init__.py -> build/lib/lobster/cli_internal/commands/light
2026-01-07T12:39:31,153   copying lobster/cli_internal/commands/light/file_commands.py -> build/lib/lobster/cli_internal/commands/light
2026-01-07T12:39:31,157   copying lobster/cli_internal/commands/light/config_commands.py -> build/lib/lobster/cli_internal/commands/light
2026-01-07T12:39:31,160   copying lobster/cli_internal/commands/light/metadata_commands.py -> build/lib/lobster/cli_internal/commands/light
2026-01-07T12:39:31,163   copying lobster/cli_internal/commands/light/pipeline_commands.py -> build/lib/lobster/cli_internal/commands/light
2026-01-07T12:39:31,167   copying lobster/cli_internal/commands/light/workspace_commands.py -> build/lib/lobster/cli_internal/commands/light
2026-01-07T12:39:31,171   creating build/lib/lobster/cli_internal/commands/heavy
2026-01-07T12:39:31,172   copying lobster/cli_internal/commands/heavy/__init__.py -> build/lib/lobster/cli_internal/commands/heavy
2026-01-07T12:39:31,175   copying lobster/cli_internal/commands/heavy/data_commands.py -> build/lib/lobster/cli_internal/commands/heavy
2026-01-07T12:39:31,178   copying lobster/cli_internal/commands/heavy/visualization_commands.py -> build/lib/lobster/cli_internal/commands/heavy
2026-01-07T12:39:31,181   copying lobster/cli_internal/commands/heavy/modality_commands.py -> build/lib/lobster/cli_internal/commands/heavy
2026-01-07T12:39:31,185   running egg_info
2026-01-07T12:39:31,197   writing lobster_ai.egg-info/PKG-INFO
2026-01-07T12:39:31,228   writing dependency_links to lobster_ai.egg-info/dependency_links.txt
2026-01-07T12:39:31,229   writing entry points to lobster_ai.egg-info/entry_points.txt
2026-01-07T12:39:31,248   writing requirements to lobster_ai.egg-info/requires.txt
2026-01-07T12:39:31,250   writing top-level names to lobster_ai.egg-info/top_level.txt
2026-01-07T12:39:31,371   reading manifest file 'lobster_ai.egg-info/SOURCES.txt'
2026-01-07T12:39:31,387   adding license file 'LICENSE'
2026-01-07T12:39:31,401   writing manifest file 'lobster_ai.egg-info/SOURCES.txt'
2026-01-07T12:39:31,494   creating build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources
2026-01-07T12:39:31,496   copying lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json -> build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources
2026-01-07T12:39:31,534   installing to build/bdist.linux-armv7l/wheel
2026-01-07T12:39:31,535   running install
2026-01-07T12:39:31,559   running install_lib
2026-01-07T12:39:31,566   creating build/bdist.linux-armv7l/wheel
2026-01-07T12:39:31,568   creating build/bdist.linux-armv7l/wheel/lobster
2026-01-07T12:39:31,570   creating build/bdist.linux-armv7l/wheel/lobster/lobster_cloud
2026-01-07T12:39:31,571   copying build/lib/lobster/lobster_cloud/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/lobster_cloud
2026-01-07T12:39:31,573   copying build/lib/lobster/lobster_cloud/client.py -> build/bdist.linux-armv7l/wheel/./lobster/lobster_cloud
2026-01-07T12:39:31,576   creating build/bdist.linux-armv7l/wheel/lobster/agents
2026-01-07T12:39:31,577   copying build/lib/lobster/agents/supervisor.py -> build/bdist.linux-armv7l/wheel/./lobster/agents
2026-01-07T12:39:31,580   copying build/lib/lobster/agents/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents
2026-01-07T12:39:31,582   copying build/lib/lobster/agents/draw_graph.py -> build/bdist.linux-armv7l/wheel/./lobster/agents
2026-01-07T12:39:31,584   creating build/bdist.linux-armv7l/wheel/lobster/agents/archive
2026-01-07T12:39:31,585   copying build/lib/lobster/agents/archive/research_agent_assistant.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/archive
2026-01-07T12:39:31,588   copying build/lib/lobster/agents/visualization_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents
2026-01-07T12:39:31,591   copying build/lib/lobster/agents/research_agent.py -> build/bdist.linux-armv7l/wheel/./lobster/agents
2026-01-07T12:39:31,596   copying build/lib/lobster/agents/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents
2026-01-07T12:39:31,599   creating build/bdist.linux-armv7l/wheel/lobster/agents/proteomics
2026-01-07T12:39:31,600   copying build/lib/lobster/agents/proteomics/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/proteomics
2026-01-07T12:39:31,603   copying build/lib/lobster/agents/proteomics/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/proteomics
2026-01-07T12:39:31,605   copying build/lib/lobster/agents/data_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents
2026-01-07T12:39:31,608   copying build/lib/lobster/agents/graph.py -> build/bdist.linux-armv7l/wheel/./lobster/agents
2026-01-07T12:39:31,611   creating build/bdist.linux-armv7l/wheel/lobster/agents/transcriptomics
2026-01-07T12:39:31,612   copying build/lib/lobster/agents/transcriptomics/transcriptomics_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics
2026-01-07T12:39:31,616   copying build/lib/lobster/agents/transcriptomics/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics
2026-01-07T12:39:31,618   copying build/lib/lobster/agents/transcriptomics/shared_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics
2026-01-07T12:39:31,620   copying build/lib/lobster/agents/transcriptomics/de_analysis_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics
2026-01-07T12:39:31,624   copying build/lib/lobster/agents/transcriptomics/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics
2026-01-07T12:39:31,626   copying build/lib/lobster/agents/transcriptomics/annotation_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics
2026-01-07T12:39:31,629   copying build/lib/lobster/agents/data_expert_assistant.py -> build/bdist.linux-armv7l/wheel/./lobster/agents
2026-01-07T12:39:31,632   creating build/bdist.linux-armv7l/wheel/lobster/agents/langgraph_supervisor
2026-01-07T12:39:31,634   copying build/lib/lobster/agents/langgraph_supervisor/supervisor.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor
2026-01-07T12:39:31,636   copying build/lib/lobster/agents/langgraph_supervisor/agent_name.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor
2026-01-07T12:39:31,639   copying build/lib/lobster/agents/langgraph_supervisor/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor
2026-01-07T12:39:31,641   copying build/lib/lobster/agents/langgraph_supervisor/handoff.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor
2026-01-07T12:39:31,643   copying build/lib/lobster/version.py -> build/bdist.linux-armv7l/wheel/./lobster
2026-01-07T12:39:31,646   creating build/bdist.linux-armv7l/wheel/lobster/core
2026-01-07T12:39:31,648   creating build/bdist.linux-armv7l/wheel/lobster/core/backends
2026-01-07T12:39:31,649   copying build/lib/lobster/core/backends/base.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends
2026-01-07T12:39:31,652   copying build/lib/lobster/core/backends/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends
2026-01-07T12:39:31,654   copying build/lib/lobster/core/backends/h5ad_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends
2026-01-07T12:39:31,657   copying build/lib/lobster/core/backends/mudata_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends
2026-01-07T12:39:31,659   copying build/lib/lobster/core/component_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,662   copying build/lib/lobster/core/download_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,664   copying build/lib/lobster/core/notebook_validator.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,667   copying build/lib/lobster/core/plot_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,669   copying build/lib/lobster/core/notebook_exporter.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,673   copying build/lib/lobster/core/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,675   copying build/lib/lobster/core/archive_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,678   copying build/lib/lobster/core/publication_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,681   copying build/lib/lobster/core/ris_parser.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,683   copying build/lib/lobster/core/notebook_executor.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,686   copying build/lib/lobster/core/provenance.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,689   copying build/lib/lobster/core/config_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,692   creating build/bdist.linux-armv7l/wheel/lobster/core/interfaces
2026-01-07T12:39:31,694   copying build/lib/lobster/core/interfaces/base_client.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces
2026-01-07T12:39:31,696   copying build/lib/lobster/core/interfaces/download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces
2026-01-07T12:39:31,700   copying build/lib/lobster/core/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces
2026-01-07T12:39:31,703   copying build/lib/lobster/core/interfaces/adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces
2026-01-07T12:39:31,707   copying build/lib/lobster/core/interfaces/backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces
2026-01-07T12:39:31,710   copying build/lib/lobster/core/interfaces/validator.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces
2026-01-07T12:39:31,713   copying build/lib/lobster/core/workspace.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,715   copying build/lib/lobster/core/client.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,720   copying build/lib/lobster/core/license_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,723   creating build/bdist.linux-armv7l/wheel/lobster/core/adapters
2026-01-07T12:39:31,725   copying build/lib/lobster/core/adapters/base.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters
2026-01-07T12:39:31,728   copying build/lib/lobster/core/adapters/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters
2026-01-07T12:39:31,729   copying build/lib/lobster/core/adapters/transcriptomics_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters
2026-01-07T12:39:31,732   copying build/lib/lobster/core/adapters/pseudobulk_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters
2026-01-07T12:39:31,735   copying build/lib/lobster/core/adapters/proteomics_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters
2026-01-07T12:39:31,738   copying build/lib/lobster/core/adapters/protein_structure_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters
2026-01-07T12:39:31,741   copying build/lib/lobster/core/exceptions.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,743   creating build/bdist.linux-armv7l/wheel/lobster/core/utils
2026-01-07T12:39:31,744   copying build/lib/lobster/core/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/utils
2026-01-07T12:39:31,746   copying build/lib/lobster/core/utils/h5ad_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/core/utils
2026-01-07T12:39:31,749   copying build/lib/lobster/core/data_manager_v2.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,754   copying build/lib/lobster/core/plugin_loader.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,757   creating build/bdist.linux-armv7l/wheel/lobster/core/identifiers
2026-01-07T12:39:31,758   copying build/lib/lobster/core/identifiers/accession_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/core/identifiers
2026-01-07T12:39:31,761   copying build/lib/lobster/core/identifiers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/identifiers
2026-01-07T12:39:31,762   copying build/lib/lobster/core/queue_storage.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,764   copying build/lib/lobster/core/ir_coverage.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,767   copying build/lib/lobster/core/analysis_ir.py -> build/bdist.linux-armv7l/wheel/./lobster/core
2026-01-07T12:39:31,770   creating build/bdist.linux-armv7l/wheel/lobster/core/schemas
2026-01-07T12:39:31,771   copying build/lib/lobster/core/schemas/transcriptomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,775   copying build/lib/lobster/core/schemas/download_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,778   copying build/lib/lobster/core/schemas/validation.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,780   copying build/lib/lobster/core/schemas/database_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,783   copying build/lib/lobster/core/schemas/metabolomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,786   copying build/lib/lobster/core/schemas/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,788   copying build/lib/lobster/core/schemas/sra.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,791   copying build/lib/lobster/core/schemas/publication_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,793   copying build/lib/lobster/core/schemas/proteomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,797   copying build/lib/lobster/core/schemas/metagenomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,800   copying build/lib/lobster/core/schemas/download_urls.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,803   copying build/lib/lobster/core/schemas/export_schemas.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,806   copying build/lib/lobster/core/schemas/database_mappings.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,809   copying build/lib/lobster/core/schemas/protein_structure.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas
2026-01-07T12:39:31,812   creating build/bdist.linux-armv7l/wheel/lobster/tools
2026-01-07T12:39:31,813   copying build/lib/lobster/tools/gpu_detector.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,816   copying build/lib/lobster/tools/geo_parser.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,818   copying build/lib/lobster/tools/custom_code_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,821   copying build/lib/lobster/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,823   copying build/lib/lobster/tools/enhanced_handoff_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,826   creating build/bdist.linux-armv7l/wheel/lobster/tools/archive
2026-01-07T12:39:31,827   copying build/lib/lobster/tools/archive/unified_content_service.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/archive
2026-01-07T12:39:31,830   copying build/lib/lobster/tools/archive/publication_service.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/archive
2026-01-07T12:39:31,833   copying build/lib/lobster/tools/expert_handoff_patterns.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,835   copying build/lib/lobster/tools/workspace_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,840   copying build/lib/lobster/tools/todo_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,843   copying build/lib/lobster/tools/workflow_tracker.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,845   copying build/lib/lobster/tools/rate_limiter.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,848   copying build/lib/lobster/tools/geo_downloader.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,850   copying build/lib/lobster/tools/pipeline_strategy.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,852   copying build/lib/lobster/tools/url_transforms.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,855   creating build/bdist.linux-armv7l/wheel/lobster/tools/providers
2026-01-07T12:39:31,856   copying build/lib/lobster/tools/providers/base_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,859   copying build/lib/lobster/tools/providers/publication_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,862   copying build/lib/lobster/tools/providers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,865   copying build/lib/lobster/tools/providers/webpage_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,867   copying build/lib/lobster/tools/providers/pride_normalizer.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,870   copying build/lib/lobster/tools/providers/geo_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,873   copying build/lib/lobster/tools/providers/biorxiv_medrxiv_config.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,875   copying build/lib/lobster/tools/providers/pubmed_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,879   copying build/lib/lobster/tools/providers/pdb_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,882   copying build/lib/lobster/tools/providers/pmc_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,885   copying build/lib/lobster/tools/providers/organism_enum.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,888   copying build/lib/lobster/tools/providers/structure_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,890   copying build/lib/lobster/tools/providers/sra_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,894   copying build/lib/lobster/tools/providers/abstract_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,896   copying build/lib/lobster/tools/providers/biopython_entrez_wrapper.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,899   copying build/lib/lobster/tools/providers/massive_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,902   copying build/lib/lobster/tools/providers/geo_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,904   copying build/lib/lobster/tools/providers/provider_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,907   copying build/lib/lobster/tools/providers/biorxiv_medrxiv_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,910   copying build/lib/lobster/tools/providers/pride_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,913   copying build/lib/lobster/tools/providers/ncbi_query_builder.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers
2026-01-07T12:39:31,916   copying build/lib/lobster/tools/handoff_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,919   copying build/lib/lobster/tools/download_orchestrator.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,921   copying build/lib/lobster/tools/expert_handoff_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/tools
2026-01-07T12:39:31,925   creating build/bdist.linux-armv7l/wheel/lobster/ui
2026-01-07T12:39:31,927   creating build/bdist.linux-armv7l/wheel/lobster/ui/callbacks
2026-01-07T12:39:31,928   copying build/lib/lobster/ui/callbacks/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/callbacks
2026-01-07T12:39:31,931   copying build/lib/lobster/ui/callbacks/textual_callback.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/callbacks
2026-01-07T12:39:31,934   copying build/lib/lobster/ui/console_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/ui
2026-01-07T12:39:31,938   creating build/bdist.linux-armv7l/wheel/lobster/ui/components
2026-01-07T12:39:31,939   copying build/lib/lobster/ui/components/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components
2026-01-07T12:39:31,941   copying build/lib/lobster/ui/components/parallel_workers_progress.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components
2026-01-07T12:39:31,945   copying build/lib/lobster/ui/components/multi_progress.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components
2026-01-07T12:39:31,948   copying build/lib/lobster/ui/components/status_display.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components
2026-01-07T12:39:31,951   copying build/lib/lobster/ui/components/file_tree.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components
2026-01-07T12:39:31,954   copying build/lib/lobster/ui/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui
2026-01-07T12:39:31,957   creating build/bdist.linux-armv7l/wheel/lobster/ui/formatters
2026-01-07T12:39:31,959   copying build/lib/lobster/ui/formatters/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/formatters
2026-01-07T12:39:31,961   copying build/lib/lobster/ui/commands.py -> build/bdist.linux-armv7l/wheel/./lobster/ui
2026-01-07T12:39:31,965   creating build/bdist.linux-armv7l/wheel/lobster/ui/screens
2026-01-07T12:39:31,967   copying build/lib/lobster/ui/screens/analysis_screen.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/screens
2026-01-07T12:39:31,970   copying build/lib/lobster/ui/screens/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/screens
2026-01-07T12:39:31,972   copying build/lib/lobster/ui/progress_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/ui
2026-01-07T12:39:31,975   copying build/lib/lobster/ui/themes.py -> build/bdist.linux-armv7l/wheel/./lobster/ui
2026-01-07T12:39:31,978   creating build/bdist.linux-armv7l/wheel/lobster/ui/services
2026-01-07T12:39:31,979   copying build/lib/lobster/ui/services/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/services
2026-01-07T12:39:31,981   copying build/lib/lobster/ui/services/error_service.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/services
2026-01-07T12:39:31,984   copying build/lib/lobster/ui/live_dashboard.py -> build/bdist.linux-armv7l/wheel/./lobster/ui
2026-01-07T12:39:31,987   copying build/lib/lobster/ui/os_app.py -> build/bdist.linux-armv7l/wheel/./lobster/ui
2026-01-07T12:39:31,990   creating build/bdist.linux-armv7l/wheel/lobster/ui/widgets
2026-01-07T12:39:31,991   copying build/lib/lobster/ui/widgets/results_display.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:31,993   copying build/lib/lobster/ui/widgets/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:31,996   copying build/lib/lobster/ui/widgets/queue_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:31,998   copying build/lib/lobster/ui/widgets/data_hub.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,001   copying build/lib/lobster/ui/widgets/status_bar.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,003   copying build/lib/lobster/ui/widgets/connections_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,005   copying build/lib/lobster/ui/widgets/plot_preview.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,008   copying build/lib/lobster/ui/widgets/activity_log.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,010   copying build/lib/lobster/ui/widgets/modality_list.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,012   copying build/lib/lobster/ui/widgets/agents_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,015   copying build/lib/lobster/ui/widgets/chat_message.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,017   copying build/lib/lobster/ui/widgets/query_prompt.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,019   copying build/lib/lobster/ui/widgets/system_info.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,021   copying build/lib/lobster/ui/widgets/token_usage_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,023   copying build/lib/lobster/ui/widgets/queue_status_bar.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,026   copying build/lib/lobster/ui/widgets/error_modal.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,028   copying build/lib/lobster/ui/widgets/adapters_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets
2026-01-07T12:39:32,030   copying build/lib/lobster/__main__.py -> build/bdist.linux-armv7l/wheel/./lobster
2026-01-07T12:39:32,032   copying build/lib/lobster/main.py -> build/bdist.linux-armv7l/wheel/./lobster
2026-01-07T12:39:32,036   copying build/lib/lobster/cli.py -> build/bdist.linux-armv7l/wheel/./lobster
2026-01-07T12:39:32,043   creating build/bdist.linux-armv7l/wheel/lobster/config
2026-01-07T12:39:32,044   copying build/lib/lobster/config/llm_factory.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,047   copying build/lib/lobster/config/agent_capabilities.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,050   copying build/lib/lobster/config/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,052   copying build/lib/lobster/config/subscription_tiers.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,054   copying build/lib/lobster/config/workspace_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,057   copying build/lib/lobster/config/base_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,059   copying build/lib/lobster/config/constants.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,061   copying build/lib/lobster/config/config_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,064   copying build/lib/lobster/config/agent_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,066   copying build/lib/lobster/config/global_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,069   copying build/lib/lobster/config/model_service.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,072   creating build/bdist.linux-armv7l/wheel/lobster/config/providers
2026-01-07T12:39:32,073   copying build/lib/lobster/config/providers/base_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers
2026-01-07T12:39:32,076   copying build/lib/lobster/config/providers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers
2026-01-07T12:39:32,078   copying build/lib/lobster/config/providers/gemini_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers
2026-01-07T12:39:32,080   copying build/lib/lobster/config/providers/registry.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers
2026-01-07T12:39:32,083   copying build/lib/lobster/config/providers/anthropic_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers
2026-01-07T12:39:32,085   copying build/lib/lobster/config/providers/ollama_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers
2026-01-07T12:39:32,088   copying build/lib/lobster/config/providers/bedrock_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers
2026-01-07T12:39:32,091   copying build/lib/lobster/config/ollama_service.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,093   copying build/lib/lobster/config/supervisor_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,096   copying build/lib/lobster/config/settings.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,098   copying build/lib/lobster/config/provider_setup.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,101   copying build/lib/lobster/config/agent_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/config
2026-01-07T12:39:32,104   creating build/bdist.linux-armv7l/wheel/lobster/services
2026-01-07T12:39:32,105   creating build/bdist.linux-armv7l/wheel/lobster/services/analysis
2026-01-07T12:39:32,107   copying build/lib/lobster/services/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis
2026-01-07T12:39:32,108   copying build/lib/lobster/services/analysis/differential_formula_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis
2026-01-07T12:39:32,111   copying build/lib/lobster/services/analysis/bulk_rnaseq_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis
2026-01-07T12:39:32,115   copying build/lib/lobster/services/analysis/enhanced_singlecell_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis
2026-01-07T12:39:32,118   copying build/lib/lobster/services/analysis/pseudobulk_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis
2026-01-07T12:39:32,121   copying build/lib/lobster/services/analysis/scvi_embedding_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis
2026-01-07T12:39:32,124   copying build/lib/lobster/services/analysis/clustering_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis
2026-01-07T12:39:32,128   copying build/lib/lobster/services/analysis/structure_analysis_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis
2026-01-07T12:39:32,131   creating build/bdist.linux-armv7l/wheel/lobster/services/data_access
2026-01-07T12:39:32,132   copying build/lib/lobster/services/data_access/geo_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,139   copying build/lib/lobster/services/data_access/workspace_content_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,142   copying build/lib/lobster/services/data_access/pride_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,145   copying build/lib/lobster/services/data_access/docling_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,148   copying build/lib/lobster/services/data_access/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,150   copying build/lib/lobster/services/data_access/protein_structure_fetch_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,153   creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo
2026-01-07T12:39:32,154   copying build/lib/lobster/services/data_access/geo/strategy.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo
2026-01-07T12:39:32,157   copying build/lib/lobster/services/data_access/geo/parser.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo
2026-01-07T12:39:32,160   copying build/lib/lobster/services/data_access/geo/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo
2026-01-07T12:39:32,163   copying build/lib/lobster/services/data_access/geo/constants.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo
2026-01-07T12:39:32,167   creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/loaders
2026-01-07T12:39:32,168   copying build/lib/lobster/services/data_access/geo/loaders/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/loaders
2026-01-07T12:39:32,170   copying build/lib/lobster/services/data_access/geo/loaders/tenx.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/loaders
2026-01-07T12:39:32,174   copying build/lib/lobster/services/data_access/geo/facade.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo
2026-01-07T12:39:32,177   creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/metadata
2026-01-07T12:39:32,179   copying build/lib/lobster/services/data_access/geo/metadata/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/metadata
2026-01-07T12:39:32,182   creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/sample
2026-01-07T12:39:32,183   copying build/lib/lobster/services/data_access/geo/sample/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/sample
2026-01-07T12:39:32,186   creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/utils
2026-01-07T12:39:32,188   copying build/lib/lobster/services/data_access/geo/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/utils
2026-01-07T12:39:32,191   copying build/lib/lobster/services/data_access/geo/downloader.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo
2026-01-07T12:39:32,196   copying build/lib/lobster/services/data_access/geo_fallback_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,200   copying build/lib/lobster/services/data_access/geo_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,203   copying build/lib/lobster/services/data_access/content_access_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,207   copying build/lib/lobster/services/data_access/sra_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,211   copying build/lib/lobster/services/data_access/massive_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access
2026-01-07T12:39:32,214   copying build/lib/lobster/services/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services
2026-01-07T12:39:32,217   creating build/bdist.linux-armv7l/wheel/lobster/services/quality
2026-01-07T12:39:32,218   copying build/lib/lobster/services/quality/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/quality
2026-01-07T12:39:32,220   copying build/lib/lobster/services/quality/preprocessing_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/quality
2026-01-07T12:39:32,224   copying build/lib/lobster/services/quality/quality_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/quality
2026-01-07T12:39:32,228   creating build/bdist.linux-armv7l/wheel/lobster/services/orchestration
2026-01-07T12:39:32,229   copying build/lib/lobster/services/orchestration/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/orchestration
2026-01-07T12:39:32,231   copying build/lib/lobster/services/orchestration/publication_processing_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/orchestration
2026-01-07T12:39:32,236   creating build/bdist.linux-armv7l/wheel/lobster/services/execution
2026-01-07T12:39:32,237   copying build/lib/lobster/services/execution/execution_context_builder.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution
2026-01-07T12:39:32,240   copying build/lib/lobster/services/execution/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution
2026-01-07T12:39:32,242   copying build/lib/lobster/services/execution/custom_code_execution_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution
2026-01-07T12:39:32,246   creating build/bdist.linux-armv7l/wheel/lobster/services/visualization
2026-01-07T12:39:32,248   copying build/lib/lobster/services/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization
2026-01-07T12:39:32,250   copying build/lib/lobster/services/visualization/pymol_visualization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization
2026-01-07T12:39:32,253   copying build/lib/lobster/services/visualization/bulk_visualization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization
2026-01-07T12:39:32,256   copying build/lib/lobster/services/visualization/visualization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization
2026-01-07T12:39:32,261   creating build/bdist.linux-armv7l/wheel/lobster/services/templates
2026-01-07T12:39:32,262   copying build/lib/lobster/services/templates/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/templates
2026-01-07T12:39:32,265   copying build/lib/lobster/services/templates/annotation_templates.py -> build/bdist.linux-armv7l/wheel/./lobster/services/templates
2026-01-07T12:39:32,269   creating build/bdist.linux-armv7l/wheel/lobster/services/data_management
2026-01-07T12:39:32,270   copying build/lib/lobster/services/data_management/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management
2026-01-07T12:39:32,272   copying build/lib/lobster/services/data_management/concatenation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management
2026-01-07T12:39:32,276   copying build/lib/lobster/services/data_management/modality_management_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management
2026-01-07T12:39:32,280   creating build/bdist.linux-armv7l/wheel/lobster/services/metadata
2026-01-07T12:39:32,282   creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction
2026-01-07T12:39:32,283   copying build/lib/lobster/services/metadata/protocol_extraction/base.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction
2026-01-07T12:39:32,286   creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/mass_spec
2026-01-07T12:39:32,288   copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec
2026-01-07T12:39:32,291   copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec
2026-01-07T12:39:32,293   copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec
2026-01-07T12:39:32,295   copying build/lib/lobster/services/metadata/protocol_extraction/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction
2026-01-07T12:39:32,298   creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/amplicon
2026-01-07T12:39:32,300   copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon
2026-01-07T12:39:32,303   copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon
2026-01-07T12:39:32,306   copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon
2026-01-07T12:39:32,309   creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/amplicon/resources
2026-01-07T12:39:32,310   copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon/resources
2026-01-07T12:39:32,314   creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/rnaseq
2026-01-07T12:39:32,315   copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq
2026-01-07T12:39:32,318   copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq
2026-01-07T12:39:32,320   copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq
2026-01-07T12:39:32,322   copying build/lib/lobster/services/metadata/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata
2026-01-07T12:39:32,324   copying build/lib/lobster/services/metadata/metadata_validation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata
2026-01-07T12:39:32,327   copying build/lib/lobster/services/metadata/identifier_provenance_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata
2026-01-07T12:39:32,330   copying build/lib/lobster/services/metadata/metadata_standardization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata
2026-01-07T12:39:32,333   copying build/lib/lobster/services/metadata/manual_annotation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata
2026-01-07T12:39:32,336   copying build/lib/lobster/services/metadata/sample_grouping_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata
2026-01-07T12:39:32,339   creating build/bdist.linux-armv7l/wheel/lobster/services/ml
2026-01-07T12:39:32,340   copying build/lib/lobster/services/ml/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/ml
2026-01-07T12:39:32,343   creating build/bdist.linux-armv7l/wheel/lobster/cli_internal
2026-01-07T12:39:32,345   copying build/lib/lobster/cli_internal/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal
2026-01-07T12:39:32,348   creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/utils
2026-01-07T12:39:32,349   copying build/lib/lobster/cli_internal/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/utils
2026-01-07T12:39:32,352   copying build/lib/lobster/cli_internal/utils/path_resolution.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/utils
2026-01-07T12:39:32,355   creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands
2026-01-07T12:39:32,357   creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands/light
2026-01-07T12:39:32,359   copying build/lib/lobster/cli_internal/commands/light/queue_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light
2026-01-07T12:39:32,362   copying build/lib/lobster/cli_internal/commands/light/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light
2026-01-07T12:39:32,364   copying build/lib/lobster/cli_internal/commands/light/file_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light
2026-01-07T12:39:32,368   copying build/lib/lobster/cli_internal/commands/light/config_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light
2026-01-07T12:39:32,371   copying build/lib/lobster/cli_internal/commands/light/metadata_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light
2026-01-07T12:39:32,373   copying build/lib/lobster/cli_internal/commands/light/pipeline_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light
2026-01-07T12:39:32,376   copying build/lib/lobster/cli_internal/commands/light/workspace_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light
2026-01-07T12:39:32,378   copying build/lib/lobster/cli_internal/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands
2026-01-07T12:39:32,381   creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands/heavy
2026-01-07T12:39:32,382   copying build/lib/lobster/cli_internal/commands/heavy/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy
2026-01-07T12:39:32,384   copying build/lib/lobster/cli_internal/commands/heavy/data_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy
2026-01-07T12:39:32,387   copying build/lib/lobster/cli_internal/commands/heavy/visualization_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy
2026-01-07T12:39:32,390   copying build/lib/lobster/cli_internal/commands/heavy/modality_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy
2026-01-07T12:39:32,393   copying build/lib/lobster/cli_internal/commands/output_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands
2026-01-07T12:39:32,397   creating build/bdist.linux-armv7l/wheel/lobster/utils
2026-01-07T12:39:32,398   copying build/lib/lobster/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,400   copying build/lib/lobster/utils/deviance.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,402   copying build/lib/lobster/utils/error_handlers.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,405   copying build/lib/lobster/utils/file_analyzer.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,408   copying build/lib/lobster/utils/json_extractor.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,411   copying build/lib/lobster/utils/logger.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,413   copying build/lib/lobster/utils/callbacks.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,416   copying build/lib/lobster/utils/progress_wrapper.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,418   copying build/lib/lobster/utils/ssl_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,421   copying build/lib/lobster/utils/system.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,423   copying build/lib/lobster/utils/file_naming.py -> build/bdist.linux-armv7l/wheel/./lobster/utils
2026-01-07T12:39:32,426   copying build/lib/lobster/_version.py -> build/bdist.linux-armv7l/wheel/./lobster
2026-01-07T12:39:32,428   running install_egg_info
2026-01-07T12:39:32,433   Copying lobster_ai.egg-info to build/bdist.linux-armv7l/wheel/./lobster_ai-0.4.0.9-py3.11.egg-info
2026-01-07T12:39:32,447   running install_scripts
2026-01-07T12:39:32,461   creating build/bdist.linux-armv7l/wheel/lobster_ai-0.4.0.9.dist-info/WHEEL
2026-01-07T12:39:32,464   creating '/tmp/pip-wheel-_u005opw/.tmp-zsm18whz/lobster_ai-0.4.0.9-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-01-07T12:39:32,467   adding 'lobster/__main__.py'
2026-01-07T12:39:32,468   adding 'lobster/_version.py'
2026-01-07T12:39:32,494   adding 'lobster/cli.py'
2026-01-07T12:39:32,497   adding 'lobster/main.py'
2026-01-07T12:39:32,498   adding 'lobster/version.py'
2026-01-07T12:39:32,500   adding 'lobster/agents/__init__.py'
2026-01-07T12:39:32,507   adding 'lobster/agents/data_expert.py'
2026-01-07T12:39:32,511   adding 'lobster/agents/data_expert_assistant.py'
2026-01-07T12:39:32,513   adding 'lobster/agents/draw_graph.py'
2026-01-07T12:39:32,515   adding 'lobster/agents/graph.py'
2026-01-07T12:39:32,529   adding 'lobster/agents/research_agent.py'
2026-01-07T12:39:32,532   adding 'lobster/agents/state.py'
2026-01-07T12:39:32,536   adding 'lobster/agents/supervisor.py'
2026-01-07T12:39:32,540   adding 'lobster/agents/visualization_expert.py'
2026-01-07T12:39:32,542   adding 'lobster/agents/archive/research_agent_assistant.py'
2026-01-07T12:39:32,544   adding 'lobster/agents/langgraph_supervisor/__init__.py'
2026-01-07T12:39:32,545   adding 'lobster/agents/langgraph_supervisor/agent_name.py'
2026-01-07T12:39:32,547   adding 'lobster/agents/langgraph_supervisor/handoff.py'
2026-01-07T12:39:32,550   adding 'lobster/agents/langgraph_supervisor/supervisor.py'
2026-01-07T12:39:32,552   adding 'lobster/agents/proteomics/__init__.py'
2026-01-07T12:39:32,553   adding 'lobster/agents/proteomics/state.py'
2026-01-07T12:39:32,555   adding 'lobster/agents/transcriptomics/__init__.py'
2026-01-07T12:39:32,560   adding 'lobster/agents/transcriptomics/annotation_expert.py'
2026-01-07T12:39:32,568   adding 'lobster/agents/transcriptomics/de_analysis_expert.py'
2026-01-07T12:39:32,572   adding 'lobster/agents/transcriptomics/shared_tools.py'
2026-01-07T12:39:32,574   adding 'lobster/agents/transcriptomics/state.py'
2026-01-07T12:39:32,579   adding 'lobster/agents/transcriptomics/transcriptomics_expert.py'
2026-01-07T12:39:32,581   adding 'lobster/cli_internal/__init__.py'
2026-01-07T12:39:32,583   adding 'lobster/cli_internal/commands/__init__.py'
2026-01-07T12:39:32,585   adding 'lobster/cli_internal/commands/output_adapter.py'
2026-01-07T12:39:32,586   adding 'lobster/cli_internal/commands/heavy/__init__.py'
2026-01-07T12:39:32,588   adding 'lobster/cli_internal/commands/heavy/data_commands.py'
2026-01-07T12:39:32,591   adding 'lobster/cli_internal/commands/heavy/modality_commands.py'
2026-01-07T12:39:32,593   adding 'lobster/cli_internal/commands/heavy/visualization_commands.py'
2026-01-07T12:39:32,595   adding 'lobster/cli_internal/commands/light/__init__.py'
2026-01-07T12:39:32,597   adding 'lobster/cli_internal/commands/light/config_commands.py'
2026-01-07T12:39:32,601   adding 'lobster/cli_internal/commands/light/file_commands.py'
2026-01-07T12:39:32,604   adding 'lobster/cli_internal/commands/light/metadata_commands.py'
2026-01-07T12:39:32,607   adding 'lobster/cli_internal/commands/light/pipeline_commands.py'
2026-01-07T12:39:32,610   adding 'lobster/cli_internal/commands/light/queue_commands.py'
2026-01-07T12:39:32,614   adding 'lobster/cli_internal/commands/light/workspace_commands.py'
2026-01-07T12:39:32,616   adding 'lobster/cli_internal/utils/__init__.py'
2026-01-07T12:39:32,618   adding 'lobster/cli_internal/utils/path_resolution.py'
2026-01-07T12:39:32,621   adding 'lobster/config/__init__.py'
2026-01-07T12:39:32,623   adding 'lobster/config/agent_capabilities.py'
2026-01-07T12:39:32,627   adding 'lobster/config/agent_config.py'
2026-01-07T12:39:32,630   adding 'lobster/config/agent_registry.py'
2026-01-07T12:39:32,632   adding 'lobster/config/base_config.py'
2026-01-07T12:39:32,635   adding 'lobster/config/config_manager.py'
2026-01-07T12:39:32,637   adding 'lobster/config/constants.py'
2026-01-07T12:39:32,639   adding 'lobster/config/global_config.py'
2026-01-07T12:39:32,642   adding 'lobster/config/llm_factory.py'
2026-01-07T12:39:32,644   adding 'lobster/config/model_service.py'
2026-01-07T12:39:32,647   adding 'lobster/config/ollama_service.py'
2026-01-07T12:39:32,649   adding 'lobster/config/provider_setup.py'
2026-01-07T12:39:32,652   adding 'lobster/config/settings.py'
2026-01-07T12:39:32,654   adding 'lobster/config/subscription_tiers.py'
2026-01-07T12:39:32,657   adding 'lobster/config/supervisor_config.py'
2026-01-07T12:39:32,659   adding 'lobster/config/workspace_config.py'
2026-01-07T12:39:32,661   adding 'lobster/config/providers/__init__.py'
2026-01-07T12:39:32,663   adding 'lobster/config/providers/anthropic_provider.py'
2026-01-07T12:39:32,665   adding 'lobster/config/providers/base_provider.py'
2026-01-07T12:39:32,668   adding 'lobster/config/providers/bedrock_provider.py'
2026-01-07T12:39:32,670   adding 'lobster/config/providers/gemini_provider.py'
2026-01-07T12:39:32,674   adding 'lobster/config/providers/ollama_provider.py'
2026-01-07T12:39:32,676   adding 'lobster/config/providers/registry.py'
2026-01-07T12:39:32,679   adding 'lobster/core/__init__.py'
2026-01-07T12:39:32,682   adding 'lobster/core/analysis_ir.py'
2026-01-07T12:39:32,686   adding 'lobster/core/archive_utils.py'
2026-01-07T12:39:32,699   adding 'lobster/core/client.py'
2026-01-07T12:39:32,702   adding 'lobster/core/component_registry.py'
2026-01-07T12:39:32,704   adding 'lobster/core/config_resolver.py'
2026-01-07T12:39:32,717   adding 'lobster/core/data_manager_v2.py'
2026-01-07T12:39:32,719   adding 'lobster/core/download_queue.py'
2026-01-07T12:39:32,721   adding 'lobster/core/exceptions.py'
2026-01-07T12:39:32,723   adding 'lobster/core/ir_coverage.py'
2026-01-07T12:39:32,726   adding 'lobster/core/license_manager.py'
2026-01-07T12:39:32,729   adding 'lobster/core/notebook_executor.py'
2026-01-07T12:39:32,732   adding 'lobster/core/notebook_exporter.py'
2026-01-07T12:39:32,734   adding 'lobster/core/notebook_validator.py'
2026-01-07T12:39:32,737   adding 'lobster/core/plot_manager.py'
2026-01-07T12:39:32,739   adding 'lobster/core/plugin_loader.py'
2026-01-07T12:39:32,741   adding 'lobster/core/provenance.py'
2026-01-07T12:39:32,744   adding 'lobster/core/publication_queue.py'
2026-01-07T12:39:32,745   adding 'lobster/core/queue_storage.py'
2026-01-07T12:39:32,747   adding 'lobster/core/ris_parser.py'
2026-01-07T12:39:32,749   adding 'lobster/core/workspace.py'
2026-01-07T12:39:32,751   adding 'lobster/core/adapters/__init__.py'
2026-01-07T12:39:32,754   adding 'lobster/core/adapters/base.py'
2026-01-07T12:39:32,756   adding 'lobster/core/adapters/protein_structure_adapter.py'
2026-01-07T12:39:32,759   adding 'lobster/core/adapters/proteomics_adapter.py'
2026-01-07T12:39:32,762   adding 'lobster/core/adapters/pseudobulk_adapter.py'
2026-01-07T12:39:32,765   adding 'lobster/core/adapters/transcriptomics_adapter.py'
2026-01-07T12:39:32,767   adding 'lobster/core/backends/__init__.py'
2026-01-07T12:39:32,769   adding 'lobster/core/backends/base.py'
2026-01-07T12:39:32,773   adding 'lobster/core/backends/h5ad_backend.py'
2026-01-07T12:39:32,775   adding 'lobster/core/backends/mudata_backend.py'
2026-01-07T12:39:32,777   adding 'lobster/core/identifiers/__init__.py'
2026-01-07T12:39:32,780   adding 'lobster/core/identifiers/accession_resolver.py'
2026-01-07T12:39:32,782   adding 'lobster/core/interfaces/__init__.py'
2026-01-07T12:39:32,784   adding 'lobster/core/interfaces/adapter.py'
2026-01-07T12:39:32,785   adding 'lobster/core/interfaces/backend.py'
2026-01-07T12:39:32,787   adding 'lobster/core/interfaces/base_client.py'
2026-01-07T12:39:32,789   adding 'lobster/core/interfaces/download_service.py'
2026-01-07T12:39:32,791   adding 'lobster/core/interfaces/validator.py'
2026-01-07T12:39:32,793   adding 'lobster/core/schemas/__init__.py'
2026-01-07T12:39:32,796   adding 'lobster/core/schemas/database_mappings.py'
2026-01-07T12:39:32,798   adding 'lobster/core/schemas/database_registry.py'
2026-01-07T12:39:32,800   adding 'lobster/core/schemas/download_queue.py'
2026-01-07T12:39:32,802   adding 'lobster/core/schemas/download_urls.py'
2026-01-07T12:39:32,807   adding 'lobster/core/schemas/export_schemas.py'
2026-01-07T12:39:32,812   adding 'lobster/core/schemas/metabolomics.py'
2026-01-07T12:39:32,817   adding 'lobster/core/schemas/metagenomics.py'
2026-01-07T12:39:32,820   adding 'lobster/core/schemas/protein_structure.py'
2026-01-07T12:39:32,824   adding 'lobster/core/schemas/proteomics.py'
2026-01-07T12:39:32,827   adding 'lobster/core/schemas/publication_queue.py'
2026-01-07T12:39:32,831   adding 'lobster/core/schemas/sra.py'
2026-01-07T12:39:32,838   adding 'lobster/core/schemas/transcriptomics.py'
2026-01-07T12:39:32,840   adding 'lobster/core/schemas/validation.py'
2026-01-07T12:39:32,842   adding 'lobster/core/utils/__init__.py'
2026-01-07T12:39:32,844   adding 'lobster/core/utils/h5ad_utils.py'
2026-01-07T12:39:32,846   adding 'lobster/lobster_cloud/__init__.py'
2026-01-07T12:39:32,848   adding 'lobster/lobster_cloud/client.py'
2026-01-07T12:39:32,849   adding 'lobster/services/__init__.py'
2026-01-07T12:39:32,851   adding 'lobster/services/analysis/__init__.py'
2026-01-07T12:39:32,859   adding 'lobster/services/analysis/bulk_rnaseq_service.py'
2026-01-07T12:39:32,868   adding 'lobster/services/analysis/clustering_service.py'
2026-01-07T12:39:32,873   adding 'lobster/services/analysis/differential_formula_service.py'
2026-01-07T12:39:32,879   adding 'lobster/services/analysis/enhanced_singlecell_service.py'
2026-01-07T12:39:32,882   adding 'lobster/services/analysis/pseudobulk_service.py'
2026-01-07T12:39:32,885   adding 'lobster/services/analysis/scvi_embedding_service.py'
2026-01-07T12:39:32,887   adding 'lobster/services/analysis/structure_analysis_service.py'
2026-01-07T12:39:32,889   adding 'lobster/services/data_access/__init__.py'
2026-01-07T12:39:32,897   adding 'lobster/services/data_access/content_access_service.py'
2026-01-07T12:39:32,904   adding 'lobster/services/data_access/docling_service.py'
2026-01-07T12:39:32,907   adding 'lobster/services/data_access/geo_download_service.py'
2026-01-07T12:39:32,910   adding 'lobster/services/data_access/geo_fallback_service.py'
2026-01-07T12:39:32,934   adding 'lobster/services/data_access/geo_service.py'
2026-01-07T12:39:32,938   adding 'lobster/services/data_access/massive_download_service.py'
2026-01-07T12:39:32,941   adding 'lobster/services/data_access/pride_download_service.py'
2026-01-07T12:39:32,943   adding 'lobster/services/data_access/protein_structure_fetch_service.py'
2026-01-07T12:39:32,948   adding 'lobster/services/data_access/sra_download_service.py'
2026-01-07T12:39:32,953   adding 'lobster/services/data_access/workspace_content_service.py'
2026-01-07T12:39:32,956   adding 'lobster/services/data_access/geo/__init__.py'
2026-01-07T12:39:32,957   adding 'lobster/services/data_access/geo/constants.py'
2026-01-07T12:39:32,961   adding 'lobster/services/data_access/geo/downloader.py'
2026-01-07T12:39:32,963   adding 'lobster/services/data_access/geo/facade.py'
2026-01-07T12:39:32,970   adding 'lobster/services/data_access/geo/parser.py'
2026-01-07T12:39:32,973   adding 'lobster/services/data_access/geo/strategy.py'
2026-01-07T12:39:32,974   adding 'lobster/services/data_access/geo/loaders/__init__.py'
2026-01-07T12:39:32,977   adding 'lobster/services/data_access/geo/loaders/tenx.py'
2026-01-07T12:39:32,978   adding 'lobster/services/data_access/geo/metadata/__init__.py'
2026-01-07T12:39:32,980   adding 'lobster/services/data_access/geo/sample/__init__.py'
2026-01-07T12:39:32,982   adding 'lobster/services/data_access/geo/utils/__init__.py'
2026-01-07T12:39:32,983   adding 'lobster/services/data_management/__init__.py'
2026-01-07T12:39:32,988   adding 'lobster/services/data_management/concatenation_service.py'
2026-01-07T12:39:32,991   adding 'lobster/services/data_management/modality_management_service.py'
2026-01-07T12:39:32,993   adding 'lobster/services/execution/__init__.py'
2026-01-07T12:39:32,997   adding 'lobster/services/execution/custom_code_execution_service.py'
2026-01-07T12:39:33,000   adding 'lobster/services/execution/execution_context_builder.py'
2026-01-07T12:39:33,002   adding 'lobster/services/metadata/__init__.py'
2026-01-07T12:39:33,003   adding 'lobster/services/metadata/identifier_provenance_service.py'
2026-01-07T12:39:33,008   adding 'lobster/services/metadata/manual_annotation_service.py'
2026-01-07T12:39:33,011   adding 'lobster/services/metadata/metadata_standardization_service.py'
2026-01-07T12:39:33,014   adding 'lobster/services/metadata/metadata_validation_service.py'
2026-01-07T12:39:33,016   adding 'lobster/services/metadata/sample_grouping_service.py'
2026-01-07T12:39:33,018   adding 'lobster/services/metadata/protocol_extraction/__init__.py'
2026-01-07T12:39:33,019   adding 'lobster/services/metadata/protocol_extraction/base.py'
2026-01-07T12:39:33,021   adding 'lobster/services/metadata/protocol_extraction/amplicon/__init__.py'
2026-01-07T12:39:33,023   adding 'lobster/services/metadata/protocol_extraction/amplicon/details.py'
2026-01-07T12:39:33,026   adding 'lobster/services/metadata/protocol_extraction/amplicon/service.py'
2026-01-07T12:39:33,028   adding 'lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json'
2026-01-07T12:39:33,030   adding 'lobster/services/metadata/protocol_extraction/mass_spec/__init__.py'
2026-01-07T12:39:33,031   adding 'lobster/services/metadata/protocol_extraction/mass_spec/details.py'
2026-01-07T12:39:33,033   adding 'lobster/services/metadata/protocol_extraction/mass_spec/service.py'
2026-01-07T12:39:33,034   adding 'lobster/services/metadata/protocol_extraction/rnaseq/__init__.py'
2026-01-07T12:39:33,036   adding 'lobster/services/metadata/protocol_extraction/rnaseq/details.py'
2026-01-07T12:39:33,037   adding 'lobster/services/metadata/protocol_extraction/rnaseq/service.py'
2026-01-07T12:39:33,039   adding 'lobster/services/ml/__init__.py'
2026-01-07T12:39:33,040   adding 'lobster/services/orchestration/__init__.py'
2026-01-07T12:39:33,049   adding 'lobster/services/orchestration/publication_processing_service.py'
2026-01-07T12:39:33,051   adding 'lobster/services/quality/__init__.py'
2026-01-07T12:39:33,056   adding 'lobster/services/quality/preprocessing_service.py'
2026-01-07T12:39:33,060   adding 'lobster/services/quality/quality_service.py'
2026-01-07T12:39:33,062   adding 'lobster/services/templates/__init__.py'
2026-01-07T12:39:33,066   adding 'lobster/services/templates/annotation_templates.py'
2026-01-07T12:39:33,068   adding 'lobster/services/visualization/__init__.py'
2026-01-07T12:39:33,071   adding 'lobster/services/visualization/bulk_visualization_service.py'
2026-01-07T12:39:33,074   adding 'lobster/services/visualization/pymol_visualization_service.py'
2026-01-07T12:39:33,082   adding 'lobster/services/visualization/visualization_service.py'
2026-01-07T12:39:33,084   adding 'lobster/tools/__init__.py'
2026-01-07T12:39:33,087   adding 'lobster/tools/custom_code_tool.py'
2026-01-07T12:39:33,089   adding 'lobster/tools/download_orchestrator.py'
2026-01-07T12:39:33,091   adding 'lobster/tools/enhanced_handoff_tool.py'
2026-01-07T12:39:33,093   adding 'lobster/tools/expert_handoff_manager.py'
2026-01-07T12:39:33,095   adding 'lobster/tools/expert_handoff_patterns.py'
2026-01-07T12:39:33,097   adding 'lobster/tools/geo_downloader.py'
2026-01-07T12:39:33,098   adding 'lobster/tools/geo_parser.py'
2026-01-07T12:39:33,100   adding 'lobster/tools/gpu_detector.py'
2026-01-07T12:39:33,101   adding 'lobster/tools/handoff_tool.py'
2026-01-07T12:39:33,103   adding 'lobster/tools/pipeline_strategy.py'
2026-01-07T12:39:33,107   adding 'lobster/tools/rate_limiter.py'
2026-01-07T12:39:33,109   adding 'lobster/tools/todo_tools.py'
2026-01-07T12:39:33,110   adding 'lobster/tools/url_transforms.py'
2026-01-07T12:39:33,113   adding 'lobster/tools/workflow_tracker.py'
2026-01-07T12:39:33,125   adding 'lobster/tools/workspace_tool.py'
2026-01-07T12:39:33,129   adding 'lobster/tools/archive/publication_service.py'
2026-01-07T12:39:33,132   adding 'lobster/tools/archive/unified_content_service.py'
2026-01-07T12:39:33,135   adding 'lobster/tools/providers/__init__.py'
2026-01-07T12:39:33,136   adding 'lobster/tools/providers/abstract_provider.py'
2026-01-07T12:39:33,139   adding 'lobster/tools/providers/base_provider.py'
2026-01-07T12:39:33,140   adding 'lobster/tools/providers/biopython_entrez_wrapper.py'
2026-01-07T12:39:33,142   adding 'lobster/tools/providers/biorxiv_medrxiv_config.py'
2026-01-07T12:39:33,148   adding 'lobster/tools/providers/biorxiv_medrxiv_provider.py'
2026-01-07T12:39:33,154   adding 'lobster/tools/providers/geo_provider.py'
2026-01-07T12:39:33,156   adding 'lobster/tools/providers/geo_utils.py'
2026-01-07T12:39:33,158   adding 'lobster/tools/providers/massive_provider.py'
2026-01-07T12:39:33,161   adding 'lobster/tools/providers/ncbi_query_builder.py'
2026-01-07T12:39:33,163   adding 'lobster/tools/providers/organism_enum.py'
2026-01-07T12:39:33,165   adding 'lobster/tools/providers/pdb_provider.py'
2026-01-07T12:39:33,172   adding 'lobster/tools/providers/pmc_provider.py'
2026-01-07T12:39:33,174   adding 'lobster/tools/providers/pride_normalizer.py'
2026-01-07T12:39:33,177   adding 'lobster/tools/providers/pride_provider.py'
2026-01-07T12:39:33,180   adding 'lobster/tools/providers/provider_registry.py'
2026-01-07T12:39:33,183   adding 'lobster/tools/providers/publication_resolver.py'
2026-01-07T12:39:33,192   adding 'lobster/tools/providers/pubmed_provider.py'
2026-01-07T12:39:33,199   adding 'lobster/tools/providers/sra_provider.py'
2026-01-07T12:39:33,201   adding 'lobster/tools/providers/structure_provider.py'
2026-01-07T12:39:33,203   adding 'lobster/tools/providers/webpage_provider.py'
2026-01-07T12:39:33,205   adding 'lobster/ui/__init__.py'
2026-01-07T12:39:33,208   adding 'lobster/ui/commands.py'
2026-01-07T12:39:33,210   adding 'lobster/ui/console_manager.py'
2026-01-07T12:39:33,212   adding 'lobster/ui/live_dashboard.py'
2026-01-07T12:39:33,214   adding 'lobster/ui/os_app.py'
2026-01-07T12:39:33,216   adding 'lobster/ui/progress_manager.py'
2026-01-07T12:39:33,218   adding 'lobster/ui/themes.py'
2026-01-07T12:39:33,220   adding 'lobster/ui/callbacks/__init__.py'
2026-01-07T12:39:33,223   adding 'lobster/ui/callbacks/textual_callback.py'
2026-01-07T12:39:33,225   adding 'lobster/ui/components/__init__.py'
2026-01-07T12:39:33,227   adding 'lobster/ui/components/file_tree.py'
2026-01-07T12:39:33,229   adding 'lobster/ui/components/multi_progress.py'
2026-01-07T12:39:33,231   adding 'lobster/ui/components/parallel_workers_progress.py'
2026-01-07T12:39:33,234   adding 'lobster/ui/components/status_display.py'
2026-01-07T12:39:33,236   adding 'lobster/ui/formatters/__init__.py'
2026-01-07T12:39:33,237   adding 'lobster/ui/screens/__init__.py'
2026-01-07T12:39:33,241   adding 'lobster/ui/screens/analysis_screen.py'
2026-01-07T12:39:33,243   adding 'lobster/ui/services/__init__.py'
2026-01-07T12:39:33,245   adding 'lobster/ui/services/error_service.py'
2026-01-07T12:39:33,247   adding 'lobster/ui/widgets/__init__.py'
2026-01-07T12:39:33,248   adding 'lobster/ui/widgets/activity_log.py'
2026-01-07T12:39:33,250   adding 'lobster/ui/widgets/adapters_panel.py'
2026-01-07T12:39:33,251   adding 'lobster/ui/widgets/agents_panel.py'
2026-01-07T12:39:33,253   adding 'lobster/ui/widgets/chat_message.py'
2026-01-07T12:39:33,254   adding 'lobster/ui/widgets/connections_panel.py'
2026-01-07T12:39:33,257   adding 'lobster/ui/widgets/data_hub.py'
2026-01-07T12:39:33,259   adding 'lobster/ui/widgets/error_modal.py'
2026-01-07T12:39:33,261   adding 'lobster/ui/widgets/modality_list.py'
2026-01-07T12:39:33,262   adding 'lobster/ui/widgets/plot_preview.py'
2026-01-07T12:39:33,263   adding 'lobster/ui/widgets/query_prompt.py'
2026-01-07T12:39:33,265   adding 'lobster/ui/widgets/queue_panel.py'
2026-01-07T12:39:33,266   adding 'lobster/ui/widgets/queue_status_bar.py'
2026-01-07T12:39:33,268   adding 'lobster/ui/widgets/results_display.py'
2026-01-07T12:39:33,270   adding 'lobster/ui/widgets/status_bar.py'
2026-01-07T12:39:33,271   adding 'lobster/ui/widgets/system_info.py'
2026-01-07T12:39:33,273   adding 'lobster/ui/widgets/token_usage_panel.py'
2026-01-07T12:39:33,275   adding 'lobster/utils/__init__.py'
2026-01-07T12:39:33,281   adding 'lobster/utils/callbacks.py'
2026-01-07T12:39:33,282   adding 'lobster/utils/deviance.py'
2026-01-07T12:39:33,285   adding 'lobster/utils/error_handlers.py'
2026-01-07T12:39:33,288   adding 'lobster/utils/file_analyzer.py'
2026-01-07T12:39:33,290   adding 'lobster/utils/file_naming.py'
2026-01-07T12:39:33,291   adding 'lobster/utils/json_extractor.py'
2026-01-07T12:39:33,292   adding 'lobster/utils/logger.py'
2026-01-07T12:39:33,294   adding 'lobster/utils/progress_wrapper.py'
2026-01-07T12:39:33,296   adding 'lobster/utils/ssl_utils.py'
2026-01-07T12:39:33,297   adding 'lobster/utils/system.py'
2026-01-07T12:39:33,304   adding 'lobster_ai-0.4.0.9.dist-info/licenses/LICENSE'
2026-01-07T12:39:33,307   adding 'lobster_ai-0.4.0.9.dist-info/METADATA'
2026-01-07T12:39:33,308   adding 'lobster_ai-0.4.0.9.dist-info/WHEEL'
2026-01-07T12:39:33,309   adding 'lobster_ai-0.4.0.9.dist-info/entry_points.txt'
2026-01-07T12:39:33,310   adding 'lobster_ai-0.4.0.9.dist-info/top_level.txt'
2026-01-07T12:39:33,314   adding 'lobster_ai-0.4.0.9.dist-info/RECORD'
2026-01-07T12:39:33,334   removing build/bdist.linux-armv7l/wheel
2026-01-07T12:39:33,516   Building wheel for lobster-ai (pyproject.toml): finished with status 'done'
2026-01-07T12:39:33,549   Created wheel for lobster-ai: filename=lobster_ai-0.4.0.9-py3-none-any.whl size=1341057 sha256=48a46075806c2941d705fa7eb0da81c1c162cc4b62b1bc22b578315363b4de75
2026-01-07T12:39:33,550   Stored in directory: /tmp/pip-ephem-wheel-cache-gbsivb5d/wheels/78/05/05/11e187e0ce5e6382ee0caac5531381b2c6425bca4712a88843
2026-01-07T12:39:33,576 Successfully built lobster-ai
2026-01-07T12:39:33,615 Removed build tracker: '/tmp/pip-build-tracker-d5teal5s'