2026-03-06T06:53:43,356 Created temporary directory: /tmp/pip-ephem-wheel-cache-kdrw29gl 2026-03-06T06:53:43,358 Created temporary directory: /tmp/pip-build-tracker-m2j5lyry 2026-03-06T06:53:43,358 Initialized build tracking at /tmp/pip-build-tracker-m2j5lyry 2026-03-06T06:53:43,359 Created build tracker: /tmp/pip-build-tracker-m2j5lyry 2026-03-06T06:53:43,359 Entered build tracker: /tmp/pip-build-tracker-m2j5lyry 2026-03-06T06:53:43,360 Created temporary directory: /tmp/pip-wheel-vmw8pg2l 2026-03-06T06:53:43,363 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. 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https://archive1.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) 2026-03-06T06:53:44,078 Skipping link: No binaries permitted for lobster-ai: https://archive1.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) 2026-03-06T06:53:44,078 Skipping link: not a file: https://www.piwheels.org/simple/lobster-ai/ 2026-03-06T06:53:44,079 Skipping link: not a file: https://pypi.org/simple/lobster-ai/ 2026-03-06T06:53:44,103 Given no hashes to check 1 links for project 'lobster-ai': discarding no candidates 2026-03-06T06:53:44,121 Collecting lobster-ai==1.1.1 2026-03-06T06:53:44,124 Created temporary directory: /tmp/pip-unpack-ex7x9nfi 2026-03-06T06:53:44,258 Downloading lobster_ai-1.1.1.tar.gz (1.3 MB) 2026-03-06T06:53:45,410 Added lobster-ai==1.1.1 from https://files.pythonhosted.org/packages/24/7f/5bdfb2bf1bd3fae98e6728c932cf2457712787c904d91884707916b2709a/lobster_ai-1.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-m2j5lyry' 2026-03-06T06:53:45,423 Created temporary directory: /tmp/pip-build-env-rhgwdk4z 2026-03-06T06:53:45,427 Installing build dependencies: started 2026-03-06T06:53:45,428 Running command pip subprocess to install build dependencies 2026-03-06T06:53:46,794 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-03-06T06:53:47,389 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 2026-03-06T06:53:47,412 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-03-06T06:53:49,175 Collecting setuptools>=65.0 2026-03-06T06:53:49,272 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.0-py3-none-any.whl (1.0 MB) 2026-03-06T06:53:49,560 Collecting wheel 2026-03-06T06:53:49,585 Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB) 2026-03-06T06:53:49,778 Collecting packaging>=24.0 2026-03-06T06:53:49,796 Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB) 2026-03-06T06:53:52,975 Installing collected packages: setuptools, packaging, wheel 2026-03-06T06:53:56,440 Creating /tmp/pip-build-env-rhgwdk4z/overlay/local/bin 2026-03-06T06:53:56,442 changing mode of /tmp/pip-build-env-rhgwdk4z/overlay/local/bin/wheel to 755 2026-03-06T06:53:56,464 Successfully installed packaging-26.0 setuptools-82.0.0 wheel-0.46.3 2026-03-06T06:53:56,741 Installing build dependencies: finished with status 'done' 2026-03-06T06:53:56,747 Getting requirements to build wheel: started 2026-03-06T06:53:56,748 Running command Getting requirements to build wheel 2026-03-06T06:53:57,445 /tmp/pip-build-env-rhgwdk4z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml` 2026-03-06T06:53:57,445 corresp(dist, value, root_dir) 2026-03-06T06:53:57,446 /tmp/pip-build-env-rhgwdk4z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-03-06T06:53:57,447 corresp(dist, value, root_dir) 2026-03-06T06:53:57,447 /tmp/pip-build-env-rhgwdk4z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies) 2026-03-06T06:53:57,448 corresp(dist, value, root_dir) 2026-03-06T06:53:57,553 running egg_info 2026-03-06T06:53:57,561 writing lobster_ai.egg-info/PKG-INFO 2026-03-06T06:53:57,587 writing dependency_links to lobster_ai.egg-info/dependency_links.txt 2026-03-06T06:53:57,590 writing entry points to lobster_ai.egg-info/entry_points.txt 2026-03-06T06:53:57,606 writing requirements to lobster_ai.egg-info/requires.txt 2026-03-06T06:53:57,608 writing top-level names to lobster_ai.egg-info/top_level.txt 2026-03-06T06:53:57,779 reading manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-03-06T06:53:57,800 adding license file 'LICENSE' 2026-03-06T06:53:57,817 writing manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-03-06T06:53:57,915 Getting requirements to build wheel: finished with status 'done' 2026-03-06T06:53:57,919 Created temporary directory: /tmp/pip-modern-metadata-7zqb3xu3 2026-03-06T06:53:57,921 Preparing metadata (pyproject.toml): started 2026-03-06T06:53:57,922 Running command Preparing metadata (pyproject.toml) 2026-03-06T06:53:58,569 /tmp/pip-build-env-rhgwdk4z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml` 2026-03-06T06:53:58,569 corresp(dist, value, root_dir) 2026-03-06T06:53:58,570 /tmp/pip-build-env-rhgwdk4z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-03-06T06:53:58,570 corresp(dist, value, root_dir) 2026-03-06T06:53:58,571 /tmp/pip-build-env-rhgwdk4z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies) 2026-03-06T06:53:58,571 corresp(dist, value, root_dir) 2026-03-06T06:53:58,666 running dist_info 2026-03-06T06:53:58,677 creating /tmp/pip-modern-metadata-7zqb3xu3/lobster_ai.egg-info 2026-03-06T06:53:58,679 writing /tmp/pip-modern-metadata-7zqb3xu3/lobster_ai.egg-info/PKG-INFO 2026-03-06T06:53:58,706 writing dependency_links to /tmp/pip-modern-metadata-7zqb3xu3/lobster_ai.egg-info/dependency_links.txt 2026-03-06T06:53:58,709 writing entry points to /tmp/pip-modern-metadata-7zqb3xu3/lobster_ai.egg-info/entry_points.txt 2026-03-06T06:53:58,725 writing requirements to /tmp/pip-modern-metadata-7zqb3xu3/lobster_ai.egg-info/requires.txt 2026-03-06T06:53:58,727 writing top-level names to /tmp/pip-modern-metadata-7zqb3xu3/lobster_ai.egg-info/top_level.txt 2026-03-06T06:53:58,729 writing manifest file '/tmp/pip-modern-metadata-7zqb3xu3/lobster_ai.egg-info/SOURCES.txt' 2026-03-06T06:53:58,888 reading manifest file '/tmp/pip-modern-metadata-7zqb3xu3/lobster_ai.egg-info/SOURCES.txt' 2026-03-06T06:53:58,890 adding license file 'LICENSE' 2026-03-06T06:53:58,903 writing manifest file '/tmp/pip-modern-metadata-7zqb3xu3/lobster_ai.egg-info/SOURCES.txt' 2026-03-06T06:53:58,905 creating '/tmp/pip-modern-metadata-7zqb3xu3/lobster_ai-1.1.1.dist-info' 2026-03-06T06:53:59,034 Preparing metadata (pyproject.toml): finished with status 'done' 2026-03-06T06:53:59,041 Source in /tmp/pip-wheel-vmw8pg2l/lobster-ai_85fc0b353b83490aa9f521de5e52c518 has version 1.1.1, which satisfies requirement lobster-ai==1.1.1 from https://files.pythonhosted.org/packages/24/7f/5bdfb2bf1bd3fae98e6728c932cf2457712787c904d91884707916b2709a/lobster_ai-1.1.1.tar.gz 2026-03-06T06:53:59,042 Removed lobster-ai==1.1.1 from https://files.pythonhosted.org/packages/24/7f/5bdfb2bf1bd3fae98e6728c932cf2457712787c904d91884707916b2709a/lobster_ai-1.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-m2j5lyry' 2026-03-06T06:53:59,054 Created temporary directory: /tmp/pip-unpack-mhkoqfw1 2026-03-06T06:53:59,055 Building wheels for collected packages: lobster-ai 2026-03-06T06:53:59,060 Created temporary directory: /tmp/pip-wheel-s6baex2_ 2026-03-06T06:53:59,060 Destination directory: /tmp/pip-wheel-s6baex2_ 2026-03-06T06:53:59,063 Building wheel for lobster-ai (pyproject.toml): started 2026-03-06T06:53:59,064 Running command Building wheel for lobster-ai (pyproject.toml) 2026-03-06T06:53:59,720 /tmp/pip-build-env-rhgwdk4z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml` 2026-03-06T06:53:59,720 corresp(dist, value, root_dir) 2026-03-06T06:53:59,721 /tmp/pip-build-env-rhgwdk4z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-03-06T06:53:59,722 corresp(dist, value, root_dir) 2026-03-06T06:53:59,723 /tmp/pip-build-env-rhgwdk4z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies) 2026-03-06T06:53:59,723 corresp(dist, value, root_dir) 2026-03-06T06:53:59,806 running bdist_wheel 2026-03-06T06:53:59,823 running build 2026-03-06T06:53:59,824 running build_py 2026-03-06T06:53:59,830 creating build/lib/lobster 2026-03-06T06:53:59,832 copying lobster/cli.py -> build/lib/lobster 2026-03-06T06:53:59,836 copying lobster/__main__.py -> build/lib/lobster 2026-03-06T06:53:59,838 copying lobster/version_cli.py -> build/lib/lobster 2026-03-06T06:53:59,840 copying lobster/version.py -> build/lib/lobster 2026-03-06T06:53:59,841 copying lobster/main.py -> build/lib/lobster 2026-03-06T06:53:59,844 creating build/lib/lobster/agents 2026-03-06T06:53:59,845 copying lobster/agents/supervisor.py -> build/lib/lobster/agents 2026-03-06T06:53:59,848 copying lobster/agents/state.py -> build/lib/lobster/agents 2026-03-06T06:53:59,850 copying lobster/agents/context_management.py -> build/lib/lobster/agents 2026-03-06T06:53:59,853 copying lobster/agents/graph.py -> build/lib/lobster/agents 2026-03-06T06:53:59,857 creating build/lib/lobster/lobster_cloud 2026-03-06T06:53:59,858 copying lobster/lobster_cloud/client.py -> build/lib/lobster/lobster_cloud 2026-03-06T06:53:59,860 copying lobster/lobster_cloud/__init__.py -> build/lib/lobster/lobster_cloud 2026-03-06T06:53:59,863 creating build/lib/lobster/core 2026-03-06T06:53:59,864 copying lobster/core/publication_queue.py -> build/lib/lobster/core 2026-03-06T06:53:59,866 copying lobster/core/sparse_utils.py -> build/lib/lobster/core 2026-03-06T06:53:59,869 copying lobster/core/config_resolver.py -> build/lib/lobster/core 2026-03-06T06:53:59,871 copying lobster/core/component_registry.py -> build/lib/lobster/core 2026-03-06T06:53:59,875 copying lobster/core/workspace.py -> build/lib/lobster/core 2026-03-06T06:53:59,878 copying lobster/core/aquadif_monitor.py -> build/lib/lobster/core 2026-03-06T06:53:59,879 copying lobster/core/protocols.py -> build/lib/lobster/core 2026-03-06T06:53:59,881 copying lobster/core/archive_utils.py -> build/lib/lobster/core 2026-03-06T06:53:59,884 copying lobster/core/plugin_loader.py -> build/lib/lobster/core 2026-03-06T06:53:59,887 copying lobster/core/extraction_cache.py -> build/lib/lobster/core 2026-03-06T06:53:59,890 copying lobster/core/notebook_exporter.py -> build/lib/lobster/core 2026-03-06T06:53:59,891 copying lobster/core/exceptions.py -> build/lib/lobster/core 2026-03-06T06:53:59,894 copying lobster/core/license_manager.py -> build/lib/lobster/core 2026-03-06T06:53:59,896 copying lobster/core/omics_registry.py -> build/lib/lobster/core 2026-03-06T06:53:59,899 copying lobster/core/ir_coverage.py -> build/lib/lobster/core 2026-03-06T06:53:59,901 copying lobster/core/lineage.py -> build/lib/lobster/core 2026-03-06T06:53:59,904 copying lobster/core/ris_parser.py -> build/lib/lobster/core 2026-03-06T06:53:59,906 copying lobster/core/client.py -> build/lib/lobster/core 2026-03-06T06:53:59,912 copying lobster/core/notebook_validator.py -> build/lib/lobster/core 2026-03-06T06:53:59,915 copying lobster/core/notebook_executor.py -> build/lib/lobster/core 2026-03-06T06:53:59,917 copying lobster/core/uv_tool_env.py -> build/lib/lobster/core 2026-03-06T06:53:59,919 copying lobster/core/plot_manager.py -> build/lib/lobster/core 2026-03-06T06:53:59,922 copying lobster/core/download_queue.py -> build/lib/lobster/core 2026-03-06T06:53:59,924 copying lobster/core/analysis_ir.py -> build/lib/lobster/core 2026-03-06T06:53:59,926 copying lobster/core/__init__.py -> build/lib/lobster/core 2026-03-06T06:53:59,928 copying lobster/core/queue_storage.py -> build/lib/lobster/core 2026-03-06T06:53:59,930 copying lobster/core/data_manager_v2.py -> build/lib/lobster/core 2026-03-06T06:53:59,933 creating build/lib/lobster/utils 2026-03-06T06:53:59,934 copying lobster/utils/llm_response_utils.py -> build/lib/lobster/utils 2026-03-06T06:53:59,936 copying lobster/utils/file_naming.py -> build/lib/lobster/utils 2026-03-06T06:53:59,938 copying lobster/utils/file_analyzer.py -> build/lib/lobster/utils 2026-03-06T06:53:59,941 copying lobster/utils/deviance.py -> build/lib/lobster/utils 2026-03-06T06:53:59,943 copying lobster/utils/system.py -> build/lib/lobster/utils 2026-03-06T06:53:59,945 copying lobster/utils/error_handlers.py -> build/lib/lobster/utils 2026-03-06T06:53:59,948 copying lobster/utils/statistics.py -> build/lib/lobster/utils 2026-03-06T06:53:59,950 copying lobster/utils/ssl_utils.py -> build/lib/lobster/utils 2026-03-06T06:53:59,953 copying lobster/utils/logger.py -> build/lib/lobster/utils 2026-03-06T06:53:59,955 copying lobster/utils/gene_annotation.py -> build/lib/lobster/utils 2026-03-06T06:53:59,958 copying lobster/utils/callbacks.py -> build/lib/lobster/utils 2026-03-06T06:53:59,962 copying lobster/utils/json_extractor.py -> build/lib/lobster/utils 2026-03-06T06:53:59,965 copying lobster/utils/progress_wrapper.py -> build/lib/lobster/utils 2026-03-06T06:53:59,967 copying lobster/utils/__init__.py -> build/lib/lobster/utils 2026-03-06T06:53:59,970 creating build/lib/lobster/cli_internal 2026-03-06T06:53:59,971 copying lobster/cli_internal/startup_diagnostics.py -> build/lib/lobster/cli_internal 2026-03-06T06:53:59,973 copying lobster/cli_internal/go_tui_launcher.py -> build/lib/lobster/cli_internal 2026-03-06T06:53:59,977 copying lobster/cli_internal/__init__.py -> build/lib/lobster/cli_internal 2026-03-06T06:53:59,980 creating build/lib/lobster/tools 2026-03-06T06:53:59,981 copying lobster/tools/custom_code_tool.py -> build/lib/lobster/tools 2026-03-06T06:53:59,984 copying lobster/tools/url_transforms.py -> build/lib/lobster/tools 2026-03-06T06:53:59,987 copying lobster/tools/store_tools.py -> build/lib/lobster/tools 2026-03-06T06:53:59,989 copying lobster/tools/pipeline_strategy.py -> build/lib/lobster/tools 2026-03-06T06:53:59,991 copying lobster/tools/knowledgebase_tools.py -> build/lib/lobster/tools 2026-03-06T06:53:59,994 copying lobster/tools/gpu_detector.py -> build/lib/lobster/tools 2026-03-06T06:53:59,997 copying lobster/tools/rate_limiter.py -> build/lib/lobster/tools 2026-03-06T06:54:00,001 copying lobster/tools/rate_limiter_arena.py -> build/lib/lobster/tools 2026-03-06T06:54:00,004 copying lobster/tools/filesystem_tools.py -> build/lib/lobster/tools 2026-03-06T06:54:00,007 copying lobster/tools/download_orchestrator.py -> build/lib/lobster/tools 2026-03-06T06:54:00,010 copying lobster/tools/workflow_tracker.py -> build/lib/lobster/tools 2026-03-06T06:54:00,013 copying lobster/tools/__init__.py -> build/lib/lobster/tools 2026-03-06T06:54:00,015 copying lobster/tools/todo_tools.py -> build/lib/lobster/tools 2026-03-06T06:54:00,018 copying lobster/tools/workspace_tool.py -> build/lib/lobster/tools 2026-03-06T06:54:00,022 creating build/lib/lobster/testing 2026-03-06T06:54:00,024 copying lobster/testing/fixtures.py -> build/lib/lobster/testing 2026-03-06T06:54:00,026 copying lobster/testing/contract_mixins.py -> build/lib/lobster/testing 2026-03-06T06:54:00,029 copying lobster/testing/mock_llm.py -> build/lib/lobster/testing 2026-03-06T06:54:00,032 copying lobster/testing/mock_data_manager.py -> build/lib/lobster/testing 2026-03-06T06:54:00,034 copying lobster/testing/__init__.py -> build/lib/lobster/testing 2026-03-06T06:54:00,036 creating build/lib/lobster/scaffold 2026-03-06T06:54:00,037 copying lobster/scaffold/validators.py -> build/lib/lobster/scaffold 2026-03-06T06:54:00,040 copying lobster/scaffold/__init__.py -> build/lib/lobster/scaffold 2026-03-06T06:54:00,042 creating build/lib/lobster/prompts 2026-03-06T06:54:00,043 copying lobster/prompts/composer.py -> build/lib/lobster/prompts 2026-03-06T06:54:00,046 copying lobster/prompts/loader.py -> build/lib/lobster/prompts 2026-03-06T06:54:00,048 copying lobster/prompts/config.py -> build/lib/lobster/prompts 2026-03-06T06:54:00,049 copying lobster/prompts/__init__.py -> build/lib/lobster/prompts 2026-03-06T06:54:00,051 copying lobster/prompts/registry.py -> build/lib/lobster/prompts 2026-03-06T06:54:00,054 creating build/lib/lobster/config 2026-03-06T06:54:00,055 copying lobster/config/constants.py -> build/lib/lobster/config 2026-03-06T06:54:00,057 copying lobster/config/settings.py -> build/lib/lobster/config 2026-03-06T06:54:00,059 copying lobster/config/global_config.py -> build/lib/lobster/config 2026-03-06T06:54:00,062 copying lobster/config/ollama_service.py -> build/lib/lobster/config 2026-03-06T06:54:00,064 copying lobster/config/provider_setup.py -> build/lib/lobster/config 2026-03-06T06:54:00,066 copying lobster/config/agent_capabilities.py -> build/lib/lobster/config 2026-03-06T06:54:00,068 copying lobster/config/subscription_tiers.py -> build/lib/lobster/config 2026-03-06T06:54:00,071 copying lobster/config/agent_presets.py -> build/lib/lobster/config 2026-03-06T06:54:00,073 copying lobster/config/agent_config_resolver.py -> build/lib/lobster/config 2026-03-06T06:54:00,075 copying lobster/config/agent_registry.py -> build/lib/lobster/config 2026-03-06T06:54:00,077 copying lobster/config/config_manager.py -> build/lib/lobster/config 2026-03-06T06:54:00,080 copying lobster/config/llm_factory.py -> build/lib/lobster/config 2026-03-06T06:54:00,083 copying lobster/config/workspace_agent_config.py -> build/lib/lobster/config 2026-03-06T06:54:00,085 copying lobster/config/aquadif.py -> build/lib/lobster/config 2026-03-06T06:54:00,087 copying lobster/config/agent_config_endpoint.py -> build/lib/lobster/config 2026-03-06T06:54:00,089 copying lobster/config/ssl_setup.py -> build/lib/lobster/config 2026-03-06T06:54:00,092 copying lobster/config/version_check.py -> build/lib/lobster/config 2026-03-06T06:54:00,094 copying lobster/config/workspace_config.py -> build/lib/lobster/config 2026-03-06T06:54:00,097 copying lobster/config/__init__.py -> build/lib/lobster/config 2026-03-06T06:54:00,099 copying lobster/config/agent_defaults.py -> build/lib/lobster/config 2026-03-06T06:54:00,101 copying lobster/config/supervisor_config.py -> build/lib/lobster/config 2026-03-06T06:54:00,103 copying lobster/config/base_config.py -> build/lib/lobster/config 2026-03-06T06:54:00,106 creating build/lib/lobster/ui 2026-03-06T06:54:00,107 copying lobster/ui/console_manager.py -> build/lib/lobster/ui 2026-03-06T06:54:00,110 copying lobster/ui/commands.py -> build/lib/lobster/ui 2026-03-06T06:54:00,113 copying lobster/ui/progress_manager.py -> build/lib/lobster/ui 2026-03-06T06:54:00,115 copying lobster/ui/themes.py -> build/lib/lobster/ui 2026-03-06T06:54:00,118 copying lobster/ui/os_app.py -> build/lib/lobster/ui 2026-03-06T06:54:00,120 copying lobster/ui/backend.py -> build/lib/lobster/ui 2026-03-06T06:54:00,122 copying lobster/ui/live_dashboard.py -> build/lib/lobster/ui 2026-03-06T06:54:00,124 copying lobster/ui/__init__.py -> build/lib/lobster/ui 2026-03-06T06:54:00,127 creating build/lib/lobster/integrations 2026-03-06T06:54:00,128 copying lobster/integrations/langchain_tui_backend.py -> build/lib/lobster/integrations 2026-03-06T06:54:00,130 copying lobster/integrations/__init__.py -> build/lib/lobster/integrations 2026-03-06T06:54:00,132 creating build/lib/lobster/core/adapters 2026-03-06T06:54:00,133 copying lobster/core/adapters/pseudobulk_adapter.py -> build/lib/lobster/core/adapters 2026-03-06T06:54:00,136 copying lobster/core/adapters/transcriptomics_adapter.py -> build/lib/lobster/core/adapters 2026-03-06T06:54:00,139 copying lobster/core/adapters/proteomics_adapter.py -> build/lib/lobster/core/adapters 2026-03-06T06:54:00,142 copying lobster/core/adapters/metabolomics_adapter.py -> build/lib/lobster/core/adapters 2026-03-06T06:54:00,145 copying lobster/core/adapters/base.py -> build/lib/lobster/core/adapters 2026-03-06T06:54:00,147 copying lobster/core/adapters/__init__.py -> build/lib/lobster/core/adapters 2026-03-06T06:54:00,149 copying lobster/core/adapters/protein_structure_adapter.py -> build/lib/lobster/core/adapters 2026-03-06T06:54:00,152 creating build/lib/lobster/core/interfaces 2026-03-06T06:54:00,153 copying lobster/core/interfaces/validator.py -> build/lib/lobster/core/interfaces 2026-03-06T06:54:00,156 copying lobster/core/interfaces/adapter.py -> build/lib/lobster/core/interfaces 2026-03-06T06:54:00,158 copying lobster/core/interfaces/queue_preparer.py -> build/lib/lobster/core/interfaces 2026-03-06T06:54:00,160 copying lobster/core/interfaces/base_client.py -> build/lib/lobster/core/interfaces 2026-03-06T06:54:00,162 copying lobster/core/interfaces/backend.py -> build/lib/lobster/core/interfaces 2026-03-06T06:54:00,165 copying lobster/core/interfaces/download_service.py -> build/lib/lobster/core/interfaces 2026-03-06T06:54:00,167 copying lobster/core/interfaces/__init__.py -> build/lib/lobster/core/interfaces 2026-03-06T06:54:00,170 creating build/lib/lobster/core/backends 2026-03-06T06:54:00,171 copying lobster/core/backends/h5ad_backend.py -> build/lib/lobster/core/backends 2026-03-06T06:54:00,174 copying lobster/core/backends/mudata_backend.py -> build/lib/lobster/core/backends 2026-03-06T06:54:00,176 copying lobster/core/backends/base.py -> build/lib/lobster/core/backends 2026-03-06T06:54:00,179 copying lobster/core/backends/__init__.py -> build/lib/lobster/core/backends 2026-03-06T06:54:00,181 creating build/lib/lobster/core/governance 2026-03-06T06:54:00,182 copying lobster/core/governance/aquadif_monitor.py -> build/lib/lobster/core/governance 2026-03-06T06:54:00,184 copying lobster/core/governance/license_manager.py -> build/lib/lobster/core/governance 2026-03-06T06:54:00,187 copying lobster/core/governance/__init__.py -> build/lib/lobster/core/governance 2026-03-06T06:54:00,189 creating build/lib/lobster/core/utils 2026-03-06T06:54:00,190 copying lobster/core/utils/h5ad_utils.py -> build/lib/lobster/core/utils 2026-03-06T06:54:00,193 copying lobster/core/utils/__init__.py -> build/lib/lobster/core/utils 2026-03-06T06:54:00,196 creating build/lib/lobster/core/identifiers 2026-03-06T06:54:00,197 copying lobster/core/identifiers/accession_resolver.py -> build/lib/lobster/core/identifiers 2026-03-06T06:54:00,200 copying lobster/core/identifiers/__init__.py -> build/lib/lobster/core/identifiers 2026-03-06T06:54:00,202 creating build/lib/lobster/core/provenance 2026-03-06T06:54:00,203 copying lobster/core/provenance/ir_coverage.py -> build/lib/lobster/core/provenance 2026-03-06T06:54:00,206 copying lobster/core/provenance/lineage.py -> build/lib/lobster/core/provenance 2026-03-06T06:54:00,208 copying lobster/core/provenance/analysis_ir.py -> build/lib/lobster/core/provenance 2026-03-06T06:54:00,211 copying lobster/core/provenance/__init__.py -> build/lib/lobster/core/provenance 2026-03-06T06:54:00,213 copying lobster/core/provenance/provenance.py -> build/lib/lobster/core/provenance 2026-03-06T06:54:00,216 creating build/lib/lobster/core/vector 2026-03-06T06:54:00,217 copying lobster/core/vector/config.py -> build/lib/lobster/core/vector 2026-03-06T06:54:00,219 copying lobster/core/vector/ontology_graph.py -> build/lib/lobster/core/vector 2026-03-06T06:54:00,221 copying lobster/core/vector/__init__.py -> build/lib/lobster/core/vector 2026-03-06T06:54:00,223 copying lobster/core/vector/service.py -> build/lib/lobster/core/vector 2026-03-06T06:54:00,225 creating build/lib/lobster/core/schemas 2026-03-06T06:54:00,226 copying lobster/core/schemas/validation.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,229 copying lobster/core/schemas/genomics.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,232 copying lobster/core/schemas/publication_queue.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,235 copying lobster/core/schemas/database_registry.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,237 copying lobster/core/schemas/database_mappings.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,240 copying lobster/core/schemas/sra.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,243 copying lobster/core/schemas/export_schemas.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,246 copying lobster/core/schemas/ontology.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,248 copying lobster/core/schemas/transcriptomics.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,252 copying lobster/core/schemas/protein_structure.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,254 copying lobster/core/schemas/metabolomics.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,257 copying lobster/core/schemas/download_urls.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,259 copying lobster/core/schemas/metagenomics.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,262 copying lobster/core/schemas/download_queue.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,265 copying lobster/core/schemas/search.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,267 copying lobster/core/schemas/clinical_schema.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,270 copying lobster/core/schemas/__init__.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,271 copying lobster/core/schemas/proteomics.py -> build/lib/lobster/core/schemas 2026-03-06T06:54:00,275 creating build/lib/lobster/core/notebooks 2026-03-06T06:54:00,276 copying lobster/core/notebooks/validator.py -> build/lib/lobster/core/notebooks 2026-03-06T06:54:00,279 copying lobster/core/notebooks/exporter.py -> build/lib/lobster/core/notebooks 2026-03-06T06:54:00,282 copying lobster/core/notebooks/executor.py -> build/lib/lobster/core/notebooks 2026-03-06T06:54:00,284 copying lobster/core/notebooks/__init__.py -> build/lib/lobster/core/notebooks 2026-03-06T06:54:00,286 creating build/lib/lobster/core/queues 2026-03-06T06:54:00,287 copying lobster/core/queues/publication_queue.py -> build/lib/lobster/core/queues 2026-03-06T06:54:00,290 copying lobster/core/queues/download_queue.py -> build/lib/lobster/core/queues 2026-03-06T06:54:00,293 copying lobster/core/queues/__init__.py -> build/lib/lobster/core/queues 2026-03-06T06:54:00,295 copying lobster/core/queues/queue_storage.py -> build/lib/lobster/core/queues 2026-03-06T06:54:00,297 creating build/lib/lobster/core/runtime 2026-03-06T06:54:00,299 copying lobster/core/runtime/workspace.py -> build/lib/lobster/core/runtime 2026-03-06T06:54:00,301 copying lobster/core/runtime/data_manager.py -> build/lib/lobster/core/runtime 2026-03-06T06:54:00,305 copying lobster/core/runtime/__init__.py -> build/lib/lobster/core/runtime 2026-03-06T06:54:00,308 creating build/lib/lobster/core/adapters/genomics 2026-03-06T06:54:00,309 copying lobster/core/adapters/genomics/vcf_adapter.py -> build/lib/lobster/core/adapters/genomics 2026-03-06T06:54:00,312 copying lobster/core/adapters/genomics/plink_adapter.py -> build/lib/lobster/core/adapters/genomics 2026-03-06T06:54:00,314 copying lobster/core/adapters/genomics/__init__.py -> build/lib/lobster/core/adapters/genomics 2026-03-06T06:54:00,317 creating build/lib/lobster/core/vector/rerankers 2026-03-06T06:54:00,318 copying lobster/core/vector/rerankers/__init__.py -> build/lib/lobster/core/vector/rerankers 2026-03-06T06:54:00,320 creating build/lib/lobster/core/vector/backends 2026-03-06T06:54:00,321 copying lobster/core/vector/backends/chromadb_backend.py -> build/lib/lobster/core/vector/backends 2026-03-06T06:54:00,323 copying lobster/core/vector/backends/base.py -> build/lib/lobster/core/vector/backends 2026-03-06T06:54:00,325 copying lobster/core/vector/backends/__init__.py -> build/lib/lobster/core/vector/backends 2026-03-06T06:54:00,327 creating build/lib/lobster/core/vector/embeddings 2026-03-06T06:54:00,328 copying lobster/core/vector/embeddings/__init__.py -> build/lib/lobster/core/vector/embeddings 2026-03-06T06:54:00,331 creating build/lib/lobster/cli_internal/utils 2026-03-06T06:54:00,332 copying lobster/cli_internal/utils/path_resolution.py -> build/lib/lobster/cli_internal/utils 2026-03-06T06:54:00,334 copying lobster/cli_internal/utils/__init__.py -> build/lib/lobster/cli_internal/utils 2026-03-06T06:54:00,337 creating build/lib/lobster/cli_internal/commands 2026-03-06T06:54:00,338 copying lobster/cli_internal/commands/output_adapter.py -> build/lib/lobster/cli_internal/commands 2026-03-06T06:54:00,340 copying lobster/cli_internal/commands/__init__.py -> build/lib/lobster/cli_internal/commands 2026-03-06T06:54:00,343 creating build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,344 copying lobster/cli_internal/commands/heavy/init_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,348 copying lobster/cli_internal/commands/heavy/slash_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,353 copying lobster/cli_internal/commands/heavy/session_infra.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,356 copying lobster/cli_internal/commands/heavy/visualization_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,358 copying lobster/cli_internal/commands/heavy/animations.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,361 copying lobster/cli_internal/commands/heavy/query_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,364 copying lobster/cli_internal/commands/heavy/data_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,366 copying lobster/cli_internal/commands/heavy/display_helpers.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,369 copying lobster/cli_internal/commands/heavy/chat_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,373 copying lobster/cli_internal/commands/heavy/__init__.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,375 copying lobster/cli_internal/commands/heavy/modality_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-03-06T06:54:00,379 creating build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,380 copying lobster/cli_internal/commands/light/validate_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,382 copying lobster/cli_internal/commands/light/pipeline_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,385 copying lobster/cli_internal/commands/light/config_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,389 copying lobster/cli_internal/commands/light/file_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,391 copying lobster/cli_internal/commands/light/scaffold_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,393 copying lobster/cli_internal/commands/light/purge_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,396 copying lobster/cli_internal/commands/light/queue_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,399 copying lobster/cli_internal/commands/light/vector_search_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,401 copying lobster/cli_internal/commands/light/metadata_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,404 copying lobster/cli_internal/commands/light/workspace_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,407 copying lobster/cli_internal/commands/light/agent_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,410 copying lobster/cli_internal/commands/light/__init__.py -> build/lib/lobster/cli_internal/commands/light 2026-03-06T06:54:00,412 creating build/lib/lobster/tools/providers 2026-03-06T06:54:00,413 copying lobster/tools/providers/pdb_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,416 copying lobster/tools/providers/sra_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,420 copying lobster/tools/providers/ncbi_query_builder.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,423 copying lobster/tools/providers/structure_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,426 copying lobster/tools/providers/pride_normalizer.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,428 copying lobster/tools/providers/pride_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,431 copying lobster/tools/providers/massive_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,433 copying lobster/tools/providers/base_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,436 copying lobster/tools/providers/provider_registry.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,438 copying lobster/tools/providers/webpage_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,441 copying lobster/tools/providers/geo_utils.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,443 copying lobster/tools/providers/biopython_entrez_wrapper.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,445 copying lobster/tools/providers/pubmed_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,450 copying lobster/tools/providers/organism_enum.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,452 copying lobster/tools/providers/pmc_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,456 copying lobster/tools/providers/metabolights_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,459 copying lobster/tools/providers/biorxiv_medrxiv_config.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,460 copying lobster/tools/providers/publication_resolver.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,463 copying lobster/tools/providers/__init__.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,465 copying lobster/tools/providers/abstract_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,468 copying lobster/tools/providers/biorxiv_medrxiv_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,471 copying lobster/tools/providers/geo_provider.py -> build/lib/lobster/tools/providers 2026-03-06T06:54:00,475 creating build/lib/lobster/scaffold/generators 2026-03-06T06:54:00,476 copying lobster/scaffold/generators/agent.py -> build/lib/lobster/scaffold/generators 2026-03-06T06:54:00,478 copying lobster/scaffold/generators/__init__.py -> build/lib/lobster/scaffold/generators 2026-03-06T06:54:00,481 creating build/lib/lobster/config/providers 2026-03-06T06:54:00,482 copying lobster/config/providers/openrouter_provider.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,485 copying lobster/config/providers/openai_provider.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,487 copying lobster/config/providers/azure_provider.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,490 copying lobster/config/providers/bedrock_provider.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,492 copying lobster/config/providers/ollama_provider.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,495 copying lobster/config/providers/base_provider.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,498 copying lobster/config/providers/gemini_provider.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,501 copying lobster/config/providers/anthropic_provider.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,505 copying lobster/config/providers/__init__.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,507 copying lobster/config/providers/registry.py -> build/lib/lobster/config/providers 2026-03-06T06:54:00,511 creating build/lib/lobster/services/orchestration 2026-03-06T06:54:00,514 copying lobster/services/orchestration/publication_processing_service.py -> build/lib/lobster/services/orchestration 2026-03-06T06:54:00,518 creating build/lib/lobster/services/metadata 2026-03-06T06:54:00,519 copying lobster/services/metadata/identifier_provenance_service.py -> build/lib/lobster/services/metadata 2026-03-06T06:54:00,522 copying lobster/services/metadata/metadata_overview_service.py -> build/lib/lobster/services/metadata 2026-03-06T06:54:00,525 copying lobster/services/metadata/metadata_validation_service.py -> build/lib/lobster/services/metadata 2026-03-06T06:54:00,529 creating build/lib/lobster/services/data_management 2026-03-06T06:54:00,530 copying lobster/services/data_management/strategy_recommendation_service.py -> build/lib/lobster/services/data_management 2026-03-06T06:54:00,535 copying lobster/services/data_management/modality_management_service.py -> build/lib/lobster/services/data_management 2026-03-06T06:54:00,538 copying lobster/services/data_management/concatenation_service.py -> build/lib/lobster/services/data_management 2026-03-06T06:54:00,542 creating build/lib/lobster/services/execution 2026-03-06T06:54:00,543 copying lobster/services/execution/execution_context_builder.py -> build/lib/lobster/services/execution 2026-03-06T06:54:00,545 copying lobster/services/execution/custom_code_execution_service.py -> build/lib/lobster/services/execution 2026-03-06T06:54:00,548 copying lobster/services/execution/sdk_delegation_service.py -> build/lib/lobster/services/execution 2026-03-06T06:54:00,551 copying lobster/services/execution/registry.py -> build/lib/lobster/services/execution 2026-03-06T06:54:00,553 creating build/lib/lobster/services/analysis 2026-03-06T06:54:00,554 copying lobster/services/analysis/bulk_rnaseq_service.py -> build/lib/lobster/services/analysis 2026-03-06T06:54:00,558 copying lobster/services/analysis/pathway_enrichment_bridge_service.py -> build/lib/lobster/services/analysis 2026-03-06T06:54:00,561 copying lobster/services/analysis/clustering_service.py -> build/lib/lobster/services/analysis 2026-03-06T06:54:00,568 copying lobster/services/analysis/pathway_enrichment_service.py -> build/lib/lobster/services/analysis 2026-03-06T06:54:00,571 creating build/lib/lobster/services/data_access 2026-03-06T06:54:00,572 copying lobster/services/data_access/sra_download_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,576 copying lobster/services/data_access/workspace_content_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,580 copying lobster/services/data_access/queue_preparation_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,583 copying lobster/services/data_access/sra_queue_preparer.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,585 copying lobster/services/data_access/content_access_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,589 copying lobster/services/data_access/docling_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,592 copying lobster/services/data_access/geo_download_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,595 copying lobster/services/data_access/metabolights_download_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,598 copying lobster/services/data_access/metabolights_queue_preparer.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,601 copying lobster/services/data_access/geo_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,603 copying lobster/services/data_access/uniprot_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,606 copying lobster/services/data_access/geo_fallback_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,608 copying lobster/services/data_access/massive_download_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,611 copying lobster/services/data_access/pride_download_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,614 copying lobster/services/data_access/geo_queue_preparer.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,617 copying lobster/services/data_access/pride_queue_preparer.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,621 copying lobster/services/data_access/ensembl_service.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,624 copying lobster/services/data_access/massive_queue_preparer.py -> build/lib/lobster/services/data_access 2026-03-06T06:54:00,627 creating build/lib/lobster/services/metadata/protocol_extraction 2026-03-06T06:54:00,629 copying lobster/services/metadata/protocol_extraction/base.py -> build/lib/lobster/services/metadata/protocol_extraction 2026-03-06T06:54:00,632 copying lobster/services/metadata/protocol_extraction/registry.py -> build/lib/lobster/services/metadata/protocol_extraction 2026-03-06T06:54:00,635 creating build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-03-06T06:54:00,637 copying lobster/services/metadata/protocol_extraction/rnaseq/details.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-03-06T06:54:00,639 copying lobster/services/metadata/protocol_extraction/rnaseq/service.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-03-06T06:54:00,643 creating build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-03-06T06:54:00,644 copying lobster/services/metadata/protocol_extraction/mass_spec/details.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-03-06T06:54:00,647 copying lobster/services/metadata/protocol_extraction/mass_spec/service.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-03-06T06:54:00,650 creating build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-03-06T06:54:00,652 copying lobster/services/metadata/protocol_extraction/amplicon/details.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-03-06T06:54:00,655 copying lobster/services/metadata/protocol_extraction/amplicon/service.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-03-06T06:54:00,660 creating build/lib/lobster/services/data_access/proteomics_parsers 2026-03-06T06:54:00,661 copying lobster/services/data_access/proteomics_parsers/file_classifier.py -> build/lib/lobster/services/data_access/proteomics_parsers 2026-03-06T06:54:00,664 copying lobster/services/data_access/proteomics_parsers/base_parser.py -> build/lib/lobster/services/data_access/proteomics_parsers 2026-03-06T06:54:00,667 copying lobster/services/data_access/proteomics_parsers/__init__.py -> build/lib/lobster/services/data_access/proteomics_parsers 2026-03-06T06:54:00,671 creating build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,673 copying lobster/services/data_access/geo/helpers.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,676 copying lobster/services/data_access/geo/downloader.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,680 copying lobster/services/data_access/geo/constants.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,683 copying lobster/services/data_access/geo/metadata_fetch.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,687 copying lobster/services/data_access/geo/concatenation.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,691 copying lobster/services/data_access/geo/download_execution.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,695 copying lobster/services/data_access/geo/archive_processing.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,699 copying lobster/services/data_access/geo/matrix_parsing.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,703 copying lobster/services/data_access/geo/facade.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,706 copying lobster/services/data_access/geo/soft_download.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,709 copying lobster/services/data_access/geo/strategy.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,714 copying lobster/services/data_access/geo/parser.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,721 copying lobster/services/data_access/geo/__init__.py -> build/lib/lobster/services/data_access/geo 2026-03-06T06:54:00,723 creating build/lib/lobster/services/data_access/geo/loaders 2026-03-06T06:54:00,724 copying lobster/services/data_access/geo/loaders/tenx.py -> build/lib/lobster/services/data_access/geo/loaders 2026-03-06T06:54:00,728 creating build/lib/lobster/ui/callbacks 2026-03-06T06:54:00,730 copying lobster/ui/callbacks/protocol_callback.py -> build/lib/lobster/ui/callbacks 2026-03-06T06:54:00,733 copying lobster/ui/callbacks/textual_callback.py -> build/lib/lobster/ui/callbacks 2026-03-06T06:54:00,736 copying lobster/ui/callbacks/__init__.py -> build/lib/lobster/ui/callbacks 2026-03-06T06:54:00,738 creating build/lib/lobster/ui/components 2026-03-06T06:54:00,740 copying lobster/ui/components/multi_progress.py -> build/lib/lobster/ui/components 2026-03-06T06:54:00,743 copying lobster/ui/components/status_display.py -> build/lib/lobster/ui/components 2026-03-06T06:54:00,746 copying lobster/ui/components/parallel_workers_progress.py -> build/lib/lobster/ui/components 2026-03-06T06:54:00,749 copying lobster/ui/components/file_tree.py -> build/lib/lobster/ui/components 2026-03-06T06:54:00,752 copying lobster/ui/components/__init__.py -> build/lib/lobster/ui/components 2026-03-06T06:54:00,755 creating build/lib/lobster/ui/widgets 2026-03-06T06:54:00,757 copying lobster/ui/widgets/system_info.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,760 copying lobster/ui/widgets/activity_log.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,762 copying lobster/ui/widgets/adapters_panel.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,764 copying lobster/ui/widgets/queue_status_bar.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,766 copying lobster/ui/widgets/modality_list.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,768 copying lobster/ui/widgets/chat_message.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,770 copying lobster/ui/widgets/data_hub.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,773 copying lobster/ui/widgets/queue_panel.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,776 copying lobster/ui/widgets/token_usage_panel.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,778 copying lobster/ui/widgets/query_prompt.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,780 copying lobster/ui/widgets/plot_preview.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,783 copying lobster/ui/widgets/results_display.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,785 copying lobster/ui/widgets/error_modal.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,787 copying lobster/ui/widgets/agents_panel.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,790 copying lobster/ui/widgets/status_bar.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,793 copying lobster/ui/widgets/__init__.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,795 copying lobster/ui/widgets/connections_panel.py -> build/lib/lobster/ui/widgets 2026-03-06T06:54:00,798 creating build/lib/lobster/ui/bridge 2026-03-06T06:54:00,799 copying lobster/ui/bridge/protocol.py -> build/lib/lobster/ui/bridge 2026-03-06T06:54:00,802 copying lobster/ui/bridge/questionary_fallback.py -> build/lib/lobster/ui/bridge 2026-03-06T06:54:00,805 copying lobster/ui/bridge/init_adapter.py -> build/lib/lobster/ui/bridge 2026-03-06T06:54:00,807 copying lobster/ui/bridge/go_tui_bridge.py -> build/lib/lobster/ui/bridge 2026-03-06T06:54:00,810 copying lobster/ui/bridge/binary_finder.py -> build/lib/lobster/ui/bridge 2026-03-06T06:54:00,812 copying lobster/ui/bridge/__init__.py -> build/lib/lobster/ui/bridge 2026-03-06T06:54:00,815 creating build/lib/lobster/ui/screens 2026-03-06T06:54:00,816 copying lobster/ui/screens/analysis_screen.py -> build/lib/lobster/ui/screens 2026-03-06T06:54:00,819 copying lobster/ui/screens/__init__.py -> build/lib/lobster/ui/screens 2026-03-06T06:54:00,821 creating build/lib/lobster/ui/formatters 2026-03-06T06:54:00,822 copying lobster/ui/formatters/__init__.py -> build/lib/lobster/ui/formatters 2026-03-06T06:54:00,824 creating build/lib/lobster/ui/services 2026-03-06T06:54:00,825 copying lobster/ui/services/error_service.py -> build/lib/lobster/ui/services 2026-03-06T06:54:00,828 copying lobster/ui/services/__init__.py -> build/lib/lobster/ui/services 2026-03-06T06:54:00,830 running egg_info 2026-03-06T06:54:00,839 writing lobster_ai.egg-info/PKG-INFO 2026-03-06T06:54:00,864 writing dependency_links to lobster_ai.egg-info/dependency_links.txt 2026-03-06T06:54:00,865 writing entry points to lobster_ai.egg-info/entry_points.txt 2026-03-06T06:54:00,882 writing requirements to lobster_ai.egg-info/requires.txt 2026-03-06T06:54:00,883 writing top-level names to lobster_ai.egg-info/top_level.txt 2026-03-06T06:54:01,243 reading manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-03-06T06:54:01,262 adding license file 'LICENSE' 2026-03-06T06:54:01,279 writing manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-03-06T06:54:01,383 creating build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources 2026-03-06T06:54:01,384 copying lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json -> build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources 2026-03-06T06:54:01,386 creating build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,387 copying lobster/scaffold/templates/prompts.py.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,390 copying lobster/scaffold/templates/agent.py.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,392 copying lobster/scaffold/templates/state.py.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,394 copying lobster/scaffold/templates/config.py.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,396 copying lobster/scaffold/templates/shared_tools.py.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,399 copying lobster/scaffold/templates/__init__.py.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,401 copying lobster/scaffold/templates/test_contract.py.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,403 copying lobster/scaffold/templates/README.md.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,405 copying lobster/scaffold/templates/conftest.py.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,408 copying lobster/scaffold/templates/pyproject.toml.j2 -> build/lib/lobster/scaffold/templates 2026-03-06T06:54:01,460 installing to build/bdist.linux-armv7l/wheel 2026-03-06T06:54:01,461 running install 2026-03-06T06:54:01,496 running install_lib 2026-03-06T06:54:01,503 creating build/bdist.linux-armv7l/wheel 2026-03-06T06:54:01,506 creating build/bdist.linux-armv7l/wheel/lobster 2026-03-06T06:54:01,507 copying build/lib/lobster/cli.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-03-06T06:54:01,512 creating build/bdist.linux-armv7l/wheel/lobster/agents 2026-03-06T06:54:01,513 copying build/lib/lobster/agents/supervisor.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-03-06T06:54:01,516 copying build/lib/lobster/agents/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-03-06T06:54:01,519 copying build/lib/lobster/agents/context_management.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-03-06T06:54:01,522 copying build/lib/lobster/agents/graph.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-03-06T06:54:01,526 creating build/bdist.linux-armv7l/wheel/lobster/lobster_cloud 2026-03-06T06:54:01,527 copying build/lib/lobster/lobster_cloud/client.py -> build/bdist.linux-armv7l/wheel/./lobster/lobster_cloud 2026-03-06T06:54:01,530 copying build/lib/lobster/lobster_cloud/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/lobster_cloud 2026-03-06T06:54:01,533 creating build/bdist.linux-armv7l/wheel/lobster/core 2026-03-06T06:54:01,534 creating build/bdist.linux-armv7l/wheel/lobster/core/adapters 2026-03-06T06:54:01,535 copying build/lib/lobster/core/adapters/pseudobulk_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-03-06T06:54:01,539 creating build/bdist.linux-armv7l/wheel/lobster/core/adapters/genomics 2026-03-06T06:54:01,540 copying build/lib/lobster/core/adapters/genomics/vcf_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters/genomics 2026-03-06T06:54:01,542 copying build/lib/lobster/core/adapters/genomics/plink_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters/genomics 2026-03-06T06:54:01,545 copying build/lib/lobster/core/adapters/genomics/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters/genomics 2026-03-06T06:54:01,547 copying build/lib/lobster/core/adapters/transcriptomics_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-03-06T06:54:01,549 copying build/lib/lobster/core/adapters/proteomics_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-03-06T06:54:01,552 copying build/lib/lobster/core/adapters/metabolomics_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-03-06T06:54:01,555 copying build/lib/lobster/core/adapters/base.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-03-06T06:54:01,558 copying build/lib/lobster/core/adapters/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-03-06T06:54:01,560 copying build/lib/lobster/core/adapters/protein_structure_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-03-06T06:54:01,563 creating build/bdist.linux-armv7l/wheel/lobster/core/interfaces 2026-03-06T06:54:01,564 copying build/lib/lobster/core/interfaces/validator.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-03-06T06:54:01,566 copying build/lib/lobster/core/interfaces/adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-03-06T06:54:01,569 copying build/lib/lobster/core/interfaces/queue_preparer.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-03-06T06:54:01,571 copying build/lib/lobster/core/interfaces/base_client.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-03-06T06:54:01,573 copying build/lib/lobster/core/interfaces/backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-03-06T06:54:01,575 copying build/lib/lobster/core/interfaces/download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-03-06T06:54:01,578 copying build/lib/lobster/core/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-03-06T06:54:01,579 copying build/lib/lobster/core/publication_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,581 copying build/lib/lobster/core/sparse_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,583 copying build/lib/lobster/core/config_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,586 copying build/lib/lobster/core/component_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,589 copying build/lib/lobster/core/workspace.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,591 creating build/bdist.linux-armv7l/wheel/lobster/core/backends 2026-03-06T06:54:01,592 copying build/lib/lobster/core/backends/h5ad_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-03-06T06:54:01,595 copying build/lib/lobster/core/backends/mudata_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-03-06T06:54:01,598 copying build/lib/lobster/core/backends/base.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-03-06T06:54:01,601 copying build/lib/lobster/core/backends/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-03-06T06:54:01,603 creating build/bdist.linux-armv7l/wheel/lobster/core/governance 2026-03-06T06:54:01,604 copying build/lib/lobster/core/governance/aquadif_monitor.py -> build/bdist.linux-armv7l/wheel/./lobster/core/governance 2026-03-06T06:54:01,607 copying build/lib/lobster/core/governance/license_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core/governance 2026-03-06T06:54:01,609 copying build/lib/lobster/core/governance/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/governance 2026-03-06T06:54:01,611 copying build/lib/lobster/core/aquadif_monitor.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,613 copying build/lib/lobster/core/protocols.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,615 copying build/lib/lobster/core/archive_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,618 creating build/bdist.linux-armv7l/wheel/lobster/core/utils 2026-03-06T06:54:01,619 copying build/lib/lobster/core/utils/h5ad_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/core/utils 2026-03-06T06:54:01,623 copying build/lib/lobster/core/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/utils 2026-03-06T06:54:01,624 copying build/lib/lobster/core/plugin_loader.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,627 copying build/lib/lobster/core/extraction_cache.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,630 copying build/lib/lobster/core/notebook_exporter.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,632 creating build/bdist.linux-armv7l/wheel/lobster/core/identifiers 2026-03-06T06:54:01,634 copying build/lib/lobster/core/identifiers/accession_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/core/identifiers 2026-03-06T06:54:01,636 copying build/lib/lobster/core/identifiers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/identifiers 2026-03-06T06:54:01,638 copying build/lib/lobster/core/exceptions.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,641 creating build/bdist.linux-armv7l/wheel/lobster/core/provenance 2026-03-06T06:54:01,642 copying build/lib/lobster/core/provenance/ir_coverage.py -> build/bdist.linux-armv7l/wheel/./lobster/core/provenance 2026-03-06T06:54:01,646 copying build/lib/lobster/core/provenance/lineage.py -> build/bdist.linux-armv7l/wheel/./lobster/core/provenance 2026-03-06T06:54:01,648 copying build/lib/lobster/core/provenance/analysis_ir.py -> build/bdist.linux-armv7l/wheel/./lobster/core/provenance 2026-03-06T06:54:01,651 copying build/lib/lobster/core/provenance/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/provenance 2026-03-06T06:54:01,653 copying build/lib/lobster/core/provenance/provenance.py -> build/bdist.linux-armv7l/wheel/./lobster/core/provenance 2026-03-06T06:54:01,656 copying build/lib/lobster/core/license_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,659 creating build/bdist.linux-armv7l/wheel/lobster/core/vector 2026-03-06T06:54:01,660 creating build/bdist.linux-armv7l/wheel/lobster/core/vector/rerankers 2026-03-06T06:54:01,662 copying build/lib/lobster/core/vector/rerankers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/vector/rerankers 2026-03-06T06:54:01,664 creating build/bdist.linux-armv7l/wheel/lobster/core/vector/backends 2026-03-06T06:54:01,665 copying build/lib/lobster/core/vector/backends/chromadb_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/vector/backends 2026-03-06T06:54:01,667 copying build/lib/lobster/core/vector/backends/base.py -> build/bdist.linux-armv7l/wheel/./lobster/core/vector/backends 2026-03-06T06:54:01,669 copying build/lib/lobster/core/vector/backends/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/vector/backends 2026-03-06T06:54:01,671 copying build/lib/lobster/core/vector/config.py -> build/bdist.linux-armv7l/wheel/./lobster/core/vector 2026-03-06T06:54:01,673 copying build/lib/lobster/core/vector/ontology_graph.py -> build/bdist.linux-armv7l/wheel/./lobster/core/vector 2026-03-06T06:54:01,676 creating build/bdist.linux-armv7l/wheel/lobster/core/vector/embeddings 2026-03-06T06:54:01,678 copying build/lib/lobster/core/vector/embeddings/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/vector/embeddings 2026-03-06T06:54:01,680 copying build/lib/lobster/core/vector/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/vector 2026-03-06T06:54:01,682 copying build/lib/lobster/core/vector/service.py -> build/bdist.linux-armv7l/wheel/./lobster/core/vector 2026-03-06T06:54:01,684 creating build/bdist.linux-armv7l/wheel/lobster/core/schemas 2026-03-06T06:54:01,685 copying build/lib/lobster/core/schemas/validation.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,688 copying build/lib/lobster/core/schemas/genomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,691 copying build/lib/lobster/core/schemas/publication_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,694 copying build/lib/lobster/core/schemas/database_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,696 copying build/lib/lobster/core/schemas/database_mappings.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,699 copying build/lib/lobster/core/schemas/sra.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,702 copying build/lib/lobster/core/schemas/export_schemas.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,705 copying build/lib/lobster/core/schemas/ontology.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,708 copying build/lib/lobster/core/schemas/transcriptomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,712 copying build/lib/lobster/core/schemas/protein_structure.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,715 copying build/lib/lobster/core/schemas/metabolomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,718 copying build/lib/lobster/core/schemas/download_urls.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,721 copying build/lib/lobster/core/schemas/metagenomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,724 copying build/lib/lobster/core/schemas/download_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,727 copying build/lib/lobster/core/schemas/search.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,729 copying build/lib/lobster/core/schemas/clinical_schema.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,732 copying build/lib/lobster/core/schemas/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,734 copying build/lib/lobster/core/schemas/proteomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-03-06T06:54:01,737 copying build/lib/lobster/core/omics_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,740 copying build/lib/lobster/core/ir_coverage.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,741 copying build/lib/lobster/core/lineage.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,743 copying build/lib/lobster/core/ris_parser.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,746 copying build/lib/lobster/core/client.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,751 copying build/lib/lobster/core/notebook_validator.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,753 creating build/bdist.linux-armv7l/wheel/lobster/core/notebooks 2026-03-06T06:54:01,755 copying build/lib/lobster/core/notebooks/validator.py -> build/bdist.linux-armv7l/wheel/./lobster/core/notebooks 2026-03-06T06:54:01,758 copying build/lib/lobster/core/notebooks/exporter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/notebooks 2026-03-06T06:54:01,761 copying build/lib/lobster/core/notebooks/executor.py -> build/bdist.linux-armv7l/wheel/./lobster/core/notebooks 2026-03-06T06:54:01,763 copying build/lib/lobster/core/notebooks/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/notebooks 2026-03-06T06:54:01,764 copying build/lib/lobster/core/notebook_executor.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,767 creating build/bdist.linux-armv7l/wheel/lobster/core/queues 2026-03-06T06:54:01,768 copying build/lib/lobster/core/queues/publication_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/queues 2026-03-06T06:54:01,771 copying build/lib/lobster/core/queues/download_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/queues 2026-03-06T06:54:01,773 copying build/lib/lobster/core/queues/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/queues 2026-03-06T06:54:01,775 copying build/lib/lobster/core/queues/queue_storage.py -> build/bdist.linux-armv7l/wheel/./lobster/core/queues 2026-03-06T06:54:01,777 copying build/lib/lobster/core/uv_tool_env.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,780 creating build/bdist.linux-armv7l/wheel/lobster/core/runtime 2026-03-06T06:54:01,781 copying build/lib/lobster/core/runtime/workspace.py -> build/bdist.linux-armv7l/wheel/./lobster/core/runtime 2026-03-06T06:54:01,783 copying build/lib/lobster/core/runtime/data_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core/runtime 2026-03-06T06:54:01,788 copying build/lib/lobster/core/runtime/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/runtime 2026-03-06T06:54:01,790 copying build/lib/lobster/core/plot_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,793 copying build/lib/lobster/core/download_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,795 copying build/lib/lobster/core/analysis_ir.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,797 copying build/lib/lobster/core/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,799 copying build/lib/lobster/core/queue_storage.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,801 copying build/lib/lobster/core/data_manager_v2.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-03-06T06:54:01,803 creating build/bdist.linux-armv7l/wheel/lobster/utils 2026-03-06T06:54:01,804 copying build/lib/lobster/utils/llm_response_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,806 copying build/lib/lobster/utils/file_naming.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,809 copying build/lib/lobster/utils/file_analyzer.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,812 copying build/lib/lobster/utils/deviance.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,813 copying build/lib/lobster/utils/system.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,816 copying build/lib/lobster/utils/error_handlers.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,819 copying build/lib/lobster/utils/statistics.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,821 copying build/lib/lobster/utils/ssl_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,823 copying build/lib/lobster/utils/logger.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,825 copying build/lib/lobster/utils/gene_annotation.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,827 copying build/lib/lobster/utils/callbacks.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,831 copying build/lib/lobster/utils/json_extractor.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,834 copying build/lib/lobster/utils/progress_wrapper.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,836 copying build/lib/lobster/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-03-06T06:54:01,838 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal 2026-03-06T06:54:01,839 copying build/lib/lobster/cli_internal/startup_diagnostics.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal 2026-03-06T06:54:01,842 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/utils 2026-03-06T06:54:01,843 copying build/lib/lobster/cli_internal/utils/path_resolution.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/utils 2026-03-06T06:54:01,845 copying build/lib/lobster/cli_internal/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/utils 2026-03-06T06:54:01,847 copying build/lib/lobster/cli_internal/go_tui_launcher.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal 2026-03-06T06:54:01,850 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands 2026-03-06T06:54:01,852 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,854 copying build/lib/lobster/cli_internal/commands/heavy/init_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,858 copying build/lib/lobster/cli_internal/commands/heavy/slash_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,865 copying build/lib/lobster/cli_internal/commands/heavy/session_infra.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,868 copying build/lib/lobster/cli_internal/commands/heavy/visualization_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,870 copying build/lib/lobster/cli_internal/commands/heavy/animations.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,872 copying build/lib/lobster/cli_internal/commands/heavy/query_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,875 copying build/lib/lobster/cli_internal/commands/heavy/data_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,877 copying build/lib/lobster/cli_internal/commands/heavy/display_helpers.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,880 copying build/lib/lobster/cli_internal/commands/heavy/chat_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,883 copying build/lib/lobster/cli_internal/commands/heavy/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,885 copying build/lib/lobster/cli_internal/commands/heavy/modality_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-03-06T06:54:01,888 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands/light 2026-03-06T06:54:01,889 copying build/lib/lobster/cli_internal/commands/light/validate_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,891 copying build/lib/lobster/cli_internal/commands/light/pipeline_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,893 copying build/lib/lobster/cli_internal/commands/light/config_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,897 copying build/lib/lobster/cli_internal/commands/light/file_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,900 copying build/lib/lobster/cli_internal/commands/light/scaffold_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,901 copying build/lib/lobster/cli_internal/commands/light/purge_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,904 copying build/lib/lobster/cli_internal/commands/light/queue_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,907 copying build/lib/lobster/cli_internal/commands/light/vector_search_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,909 copying build/lib/lobster/cli_internal/commands/light/metadata_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,912 copying build/lib/lobster/cli_internal/commands/light/workspace_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,915 copying build/lib/lobster/cli_internal/commands/light/agent_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,918 copying build/lib/lobster/cli_internal/commands/light/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-03-06T06:54:01,919 copying build/lib/lobster/cli_internal/commands/output_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-03-06T06:54:01,922 copying build/lib/lobster/cli_internal/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-03-06T06:54:01,924 copying build/lib/lobster/cli_internal/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal 2026-03-06T06:54:01,926 creating build/bdist.linux-armv7l/wheel/lobster/tools 2026-03-06T06:54:01,927 copying build/lib/lobster/tools/custom_code_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:01,930 copying build/lib/lobster/tools/url_transforms.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:01,931 copying build/lib/lobster/tools/store_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:01,933 copying build/lib/lobster/tools/pipeline_strategy.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:01,935 copying build/lib/lobster/tools/knowledgebase_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:01,938 copying build/lib/lobster/tools/gpu_detector.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:01,940 copying build/lib/lobster/tools/rate_limiter.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:01,944 creating build/bdist.linux-armv7l/wheel/lobster/tools/providers 2026-03-06T06:54:01,945 copying build/lib/lobster/tools/providers/pdb_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,947 copying build/lib/lobster/tools/providers/sra_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,951 copying build/lib/lobster/tools/providers/ncbi_query_builder.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,954 copying build/lib/lobster/tools/providers/structure_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,956 copying build/lib/lobster/tools/providers/pride_normalizer.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,959 copying build/lib/lobster/tools/providers/pride_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,962 copying build/lib/lobster/tools/providers/massive_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,964 copying build/lib/lobster/tools/providers/base_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,967 copying build/lib/lobster/tools/providers/provider_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,969 copying build/lib/lobster/tools/providers/webpage_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,971 copying build/lib/lobster/tools/providers/geo_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,973 copying build/lib/lobster/tools/providers/biopython_entrez_wrapper.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,976 copying build/lib/lobster/tools/providers/pubmed_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,979 copying build/lib/lobster/tools/providers/organism_enum.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,981 copying build/lib/lobster/tools/providers/pmc_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,984 copying build/lib/lobster/tools/providers/metabolights_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,988 copying build/lib/lobster/tools/providers/biorxiv_medrxiv_config.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,990 copying build/lib/lobster/tools/providers/publication_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,993 copying build/lib/lobster/tools/providers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,995 copying build/lib/lobster/tools/providers/abstract_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:01,997 copying build/lib/lobster/tools/providers/biorxiv_medrxiv_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:02,001 copying build/lib/lobster/tools/providers/geo_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-03-06T06:54:02,004 copying build/lib/lobster/tools/rate_limiter_arena.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:02,006 copying build/lib/lobster/tools/filesystem_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:02,009 copying build/lib/lobster/tools/download_orchestrator.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:02,011 copying build/lib/lobster/tools/workflow_tracker.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:02,013 copying build/lib/lobster/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:02,015 copying build/lib/lobster/tools/todo_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:02,017 copying build/lib/lobster/tools/workspace_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-03-06T06:54:02,021 creating build/bdist.linux-armv7l/wheel/lobster/testing 2026-03-06T06:54:02,022 copying build/lib/lobster/testing/fixtures.py -> build/bdist.linux-armv7l/wheel/./lobster/testing 2026-03-06T06:54:02,025 copying build/lib/lobster/testing/contract_mixins.py -> build/bdist.linux-armv7l/wheel/./lobster/testing 2026-03-06T06:54:02,028 copying build/lib/lobster/testing/mock_llm.py -> build/bdist.linux-armv7l/wheel/./lobster/testing 2026-03-06T06:54:02,030 copying build/lib/lobster/testing/mock_data_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/testing 2026-03-06T06:54:02,032 copying build/lib/lobster/testing/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/testing 2026-03-06T06:54:02,035 creating build/bdist.linux-armv7l/wheel/lobster/scaffold 2026-03-06T06:54:02,036 copying build/lib/lobster/scaffold/validators.py -> build/bdist.linux-armv7l/wheel/./lobster/scaffold 2026-03-06T06:54:02,040 creating build/bdist.linux-armv7l/wheel/lobster/scaffold/generators 2026-03-06T06:54:02,041 copying build/lib/lobster/scaffold/generators/agent.py -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/generators 2026-03-06T06:54:02,043 copying build/lib/lobster/scaffold/generators/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/generators 2026-03-06T06:54:02,046 creating build/bdist.linux-armv7l/wheel/lobster/scaffold/templates 2026-03-06T06:54:02,047 copying build/lib/lobster/scaffold/templates/prompts.py.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,049 copying build/lib/lobster/scaffold/templates/agent.py.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,051 copying build/lib/lobster/scaffold/templates/state.py.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,053 copying build/lib/lobster/scaffold/templates/config.py.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,055 copying build/lib/lobster/scaffold/templates/shared_tools.py.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,057 copying build/lib/lobster/scaffold/templates/__init__.py.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,059 copying build/lib/lobster/scaffold/templates/test_contract.py.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,061 copying build/lib/lobster/scaffold/templates/README.md.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,063 copying build/lib/lobster/scaffold/templates/conftest.py.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,064 copying build/lib/lobster/scaffold/templates/pyproject.toml.j2 -> build/bdist.linux-armv7l/wheel/./lobster/scaffold/templates 2026-03-06T06:54:02,067 copying build/lib/lobster/scaffold/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/scaffold 2026-03-06T06:54:02,069 copying build/lib/lobster/__main__.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-03-06T06:54:02,072 creating build/bdist.linux-armv7l/wheel/lobster/prompts 2026-03-06T06:54:02,074 copying build/lib/lobster/prompts/composer.py -> build/bdist.linux-armv7l/wheel/./lobster/prompts 2026-03-06T06:54:02,077 copying build/lib/lobster/prompts/loader.py -> build/bdist.linux-armv7l/wheel/./lobster/prompts 2026-03-06T06:54:02,079 copying build/lib/lobster/prompts/config.py -> build/bdist.linux-armv7l/wheel/./lobster/prompts 2026-03-06T06:54:02,081 copying build/lib/lobster/prompts/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/prompts 2026-03-06T06:54:02,083 copying build/lib/lobster/prompts/registry.py -> build/bdist.linux-armv7l/wheel/./lobster/prompts 2026-03-06T06:54:02,085 creating build/bdist.linux-armv7l/wheel/lobster/config 2026-03-06T06:54:02,086 copying build/lib/lobster/config/constants.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,088 copying build/lib/lobster/config/settings.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,091 copying build/lib/lobster/config/global_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,093 copying build/lib/lobster/config/ollama_service.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,096 copying build/lib/lobster/config/provider_setup.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,098 copying build/lib/lobster/config/agent_capabilities.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,101 copying build/lib/lobster/config/subscription_tiers.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,103 copying build/lib/lobster/config/agent_presets.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,105 copying build/lib/lobster/config/agent_config_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,108 copying build/lib/lobster/config/agent_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,110 copying build/lib/lobster/config/config_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,112 copying build/lib/lobster/config/llm_factory.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,114 copying build/lib/lobster/config/workspace_agent_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,116 copying build/lib/lobster/config/aquadif.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,119 creating build/bdist.linux-armv7l/wheel/lobster/config/providers 2026-03-06T06:54:02,120 copying build/lib/lobster/config/providers/openrouter_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,123 copying build/lib/lobster/config/providers/openai_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,125 copying build/lib/lobster/config/providers/azure_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,128 copying build/lib/lobster/config/providers/bedrock_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,130 copying build/lib/lobster/config/providers/ollama_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,133 copying build/lib/lobster/config/providers/base_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,135 copying build/lib/lobster/config/providers/gemini_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,137 copying build/lib/lobster/config/providers/anthropic_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,139 copying build/lib/lobster/config/providers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,141 copying build/lib/lobster/config/providers/registry.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-03-06T06:54:02,143 copying build/lib/lobster/config/agent_config_endpoint.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,145 copying build/lib/lobster/config/ssl_setup.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,148 copying build/lib/lobster/config/version_check.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,151 copying build/lib/lobster/config/workspace_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,154 copying build/lib/lobster/config/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,156 copying build/lib/lobster/config/agent_defaults.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,159 copying build/lib/lobster/config/supervisor_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,161 copying build/lib/lobster/config/base_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-03-06T06:54:02,164 creating build/bdist.linux-armv7l/wheel/lobster/services 2026-03-06T06:54:02,165 creating build/bdist.linux-armv7l/wheel/lobster/services/orchestration 2026-03-06T06:54:02,167 copying build/lib/lobster/services/orchestration/publication_processing_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/orchestration 2026-03-06T06:54:02,171 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata 2026-03-06T06:54:02,172 copying build/lib/lobster/services/metadata/identifier_provenance_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-03-06T06:54:02,174 copying build/lib/lobster/services/metadata/metadata_overview_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-03-06T06:54:02,177 copying build/lib/lobster/services/metadata/metadata_validation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-03-06T06:54:02,180 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction 2026-03-06T06:54:02,182 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/rnaseq 2026-03-06T06:54:02,183 copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq 2026-03-06T06:54:02,185 copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq 2026-03-06T06:54:02,188 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/mass_spec 2026-03-06T06:54:02,189 copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec 2026-03-06T06:54:02,191 copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec 2026-03-06T06:54:02,193 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/amplicon 2026-03-06T06:54:02,195 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/amplicon/resources 2026-03-06T06:54:02,196 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon/resources 2026-03-06T06:54:02,199 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon 2026-03-06T06:54:02,201 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon 2026-03-06T06:54:02,204 copying build/lib/lobster/services/metadata/protocol_extraction/base.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction 2026-03-06T06:54:02,206 copying build/lib/lobster/services/metadata/protocol_extraction/registry.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction 2026-03-06T06:54:02,209 creating build/bdist.linux-armv7l/wheel/lobster/services/data_management 2026-03-06T06:54:02,210 copying build/lib/lobster/services/data_management/strategy_recommendation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-03-06T06:54:02,212 copying build/lib/lobster/services/data_management/modality_management_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-03-06T06:54:02,215 copying build/lib/lobster/services/data_management/concatenation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-03-06T06:54:02,218 creating build/bdist.linux-armv7l/wheel/lobster/services/execution 2026-03-06T06:54:02,219 copying build/lib/lobster/services/execution/execution_context_builder.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-03-06T06:54:02,222 copying build/lib/lobster/services/execution/custom_code_execution_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-03-06T06:54:02,226 copying build/lib/lobster/services/execution/sdk_delegation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-03-06T06:54:02,231 copying build/lib/lobster/services/execution/registry.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-03-06T06:54:02,235 creating build/bdist.linux-armv7l/wheel/lobster/services/analysis 2026-03-06T06:54:02,237 copying build/lib/lobster/services/analysis/bulk_rnaseq_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-03-06T06:54:02,243 copying build/lib/lobster/services/analysis/pathway_enrichment_bridge_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-03-06T06:54:02,247 copying build/lib/lobster/services/analysis/clustering_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-03-06T06:54:02,254 copying build/lib/lobster/services/analysis/pathway_enrichment_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-03-06T06:54:02,258 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access 2026-03-06T06:54:02,260 copying build/lib/lobster/services/data_access/sra_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,264 copying build/lib/lobster/services/data_access/workspace_content_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,267 copying build/lib/lobster/services/data_access/queue_preparation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,270 copying build/lib/lobster/services/data_access/sra_queue_preparer.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,273 copying build/lib/lobster/services/data_access/content_access_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,278 copying build/lib/lobster/services/data_access/docling_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,282 copying build/lib/lobster/services/data_access/geo_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,285 copying build/lib/lobster/services/data_access/metabolights_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,288 copying build/lib/lobster/services/data_access/metabolights_queue_preparer.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,291 copying build/lib/lobster/services/data_access/geo_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,294 copying build/lib/lobster/services/data_access/uniprot_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,297 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/proteomics_parsers 2026-03-06T06:54:02,299 copying build/lib/lobster/services/data_access/proteomics_parsers/file_classifier.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/proteomics_parsers 2026-03-06T06:54:02,303 copying build/lib/lobster/services/data_access/proteomics_parsers/base_parser.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/proteomics_parsers 2026-03-06T06:54:02,306 copying build/lib/lobster/services/data_access/proteomics_parsers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/proteomics_parsers 2026-03-06T06:54:02,310 copying build/lib/lobster/services/data_access/geo_fallback_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,315 copying build/lib/lobster/services/data_access/massive_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,320 copying build/lib/lobster/services/data_access/pride_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,324 copying build/lib/lobster/services/data_access/geo_queue_preparer.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,329 copying build/lib/lobster/services/data_access/pride_queue_preparer.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,332 copying build/lib/lobster/services/data_access/ensembl_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,337 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo 2026-03-06T06:54:02,339 copying build/lib/lobster/services/data_access/geo/helpers.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,343 copying build/lib/lobster/services/data_access/geo/downloader.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,347 copying build/lib/lobster/services/data_access/geo/constants.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,350 copying build/lib/lobster/services/data_access/geo/metadata_fetch.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,354 copying build/lib/lobster/services/data_access/geo/concatenation.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,357 copying build/lib/lobster/services/data_access/geo/download_execution.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,362 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/loaders 2026-03-06T06:54:02,364 copying build/lib/lobster/services/data_access/geo/loaders/tenx.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/loaders 2026-03-06T06:54:02,368 copying build/lib/lobster/services/data_access/geo/archive_processing.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,372 copying build/lib/lobster/services/data_access/geo/matrix_parsing.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,376 copying build/lib/lobster/services/data_access/geo/facade.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,379 copying build/lib/lobster/services/data_access/geo/soft_download.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,383 copying build/lib/lobster/services/data_access/geo/strategy.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,388 copying build/lib/lobster/services/data_access/geo/parser.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,394 copying build/lib/lobster/services/data_access/geo/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-03-06T06:54:02,397 copying build/lib/lobster/services/data_access/massive_queue_preparer.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-03-06T06:54:02,401 creating build/bdist.linux-armv7l/wheel/lobster/ui 2026-03-06T06:54:02,404 creating build/bdist.linux-armv7l/wheel/lobster/ui/callbacks 2026-03-06T06:54:02,406 copying build/lib/lobster/ui/callbacks/protocol_callback.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/callbacks 2026-03-06T06:54:02,411 copying build/lib/lobster/ui/callbacks/textual_callback.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/callbacks 2026-03-06T06:54:02,416 copying build/lib/lobster/ui/callbacks/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/callbacks 2026-03-06T06:54:02,423 creating build/bdist.linux-armv7l/wheel/lobster/ui/components 2026-03-06T06:54:02,425 copying build/lib/lobster/ui/components/multi_progress.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-03-06T06:54:02,434 copying build/lib/lobster/ui/components/status_display.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-03-06T06:54:02,443 copying build/lib/lobster/ui/components/parallel_workers_progress.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-03-06T06:54:02,447 copying build/lib/lobster/ui/components/file_tree.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-03-06T06:54:02,450 copying build/lib/lobster/ui/components/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-03-06T06:54:02,453 creating build/bdist.linux-armv7l/wheel/lobster/ui/widgets 2026-03-06T06:54:02,455 copying build/lib/lobster/ui/widgets/system_info.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,457 copying build/lib/lobster/ui/widgets/activity_log.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,460 copying build/lib/lobster/ui/widgets/adapters_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,463 copying build/lib/lobster/ui/widgets/queue_status_bar.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,466 copying build/lib/lobster/ui/widgets/modality_list.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,468 copying build/lib/lobster/ui/widgets/chat_message.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,470 copying build/lib/lobster/ui/widgets/data_hub.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,473 copying build/lib/lobster/ui/widgets/queue_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,476 copying build/lib/lobster/ui/widgets/token_usage_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,479 copying build/lib/lobster/ui/widgets/query_prompt.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,483 copying build/lib/lobster/ui/widgets/plot_preview.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,487 copying build/lib/lobster/ui/widgets/results_display.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,492 copying build/lib/lobster/ui/widgets/error_modal.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,496 copying build/lib/lobster/ui/widgets/agents_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,500 copying build/lib/lobster/ui/widgets/status_bar.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,504 copying build/lib/lobster/ui/widgets/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,506 copying build/lib/lobster/ui/widgets/connections_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-03-06T06:54:02,510 copying build/lib/lobster/ui/console_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-03-06T06:54:02,516 creating build/bdist.linux-armv7l/wheel/lobster/ui/bridge 2026-03-06T06:54:02,518 copying build/lib/lobster/ui/bridge/protocol.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/bridge 2026-03-06T06:54:02,521 copying build/lib/lobster/ui/bridge/questionary_fallback.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/bridge 2026-03-06T06:54:02,526 copying build/lib/lobster/ui/bridge/init_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/bridge 2026-03-06T06:54:02,530 copying build/lib/lobster/ui/bridge/go_tui_bridge.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/bridge 2026-03-06T06:54:02,533 copying build/lib/lobster/ui/bridge/binary_finder.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/bridge 2026-03-06T06:54:02,535 copying build/lib/lobster/ui/bridge/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/bridge 2026-03-06T06:54:02,538 copying build/lib/lobster/ui/commands.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-03-06T06:54:02,542 creating build/bdist.linux-armv7l/wheel/lobster/ui/screens 2026-03-06T06:54:02,543 copying build/lib/lobster/ui/screens/analysis_screen.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/screens 2026-03-06T06:54:02,547 copying build/lib/lobster/ui/screens/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/screens 2026-03-06T06:54:02,550 copying build/lib/lobster/ui/progress_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-03-06T06:54:02,554 copying build/lib/lobster/ui/themes.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-03-06T06:54:02,557 copying build/lib/lobster/ui/os_app.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-03-06T06:54:02,561 creating build/bdist.linux-armv7l/wheel/lobster/ui/formatters 2026-03-06T06:54:02,562 copying build/lib/lobster/ui/formatters/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/formatters 2026-03-06T06:54:02,565 copying build/lib/lobster/ui/backend.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-03-06T06:54:02,568 creating build/bdist.linux-armv7l/wheel/lobster/ui/services 2026-03-06T06:54:02,570 copying build/lib/lobster/ui/services/error_service.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/services 2026-03-06T06:54:02,573 copying build/lib/lobster/ui/services/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/services 2026-03-06T06:54:02,576 copying build/lib/lobster/ui/live_dashboard.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-03-06T06:54:02,580 copying build/lib/lobster/ui/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-03-06T06:54:02,582 copying build/lib/lobster/version_cli.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-03-06T06:54:02,584 copying build/lib/lobster/version.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-03-06T06:54:02,586 copying build/lib/lobster/main.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-03-06T06:54:02,589 creating build/bdist.linux-armv7l/wheel/lobster/integrations 2026-03-06T06:54:02,590 copying build/lib/lobster/integrations/langchain_tui_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/integrations 2026-03-06T06:54:02,593 copying build/lib/lobster/integrations/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/integrations 2026-03-06T06:54:02,595 running install_egg_info 2026-03-06T06:54:02,603 Copying lobster_ai.egg-info to build/bdist.linux-armv7l/wheel/./lobster_ai-1.1.1-py3.11.egg-info 2026-03-06T06:54:02,619 running install_scripts 2026-03-06T06:54:02,634 creating build/bdist.linux-armv7l/wheel/lobster_ai-1.1.1.dist-info/WHEEL 2026-03-06T06:54:02,637 creating '/tmp/pip-wheel-s6baex2_/.tmp-5o81yxaa/lobster_ai-1.1.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-03-06T06:54:02,640 adding 'lobster/__main__.py' 2026-03-06T06:54:02,646 adding 'lobster/cli.py' 2026-03-06T06:54:02,647 adding 'lobster/main.py' 2026-03-06T06:54:02,649 adding 'lobster/version.py' 2026-03-06T06:54:02,650 adding 'lobster/version_cli.py' 2026-03-06T06:54:02,652 adding 'lobster/agents/context_management.py' 2026-03-06T06:54:02,657 adding 'lobster/agents/graph.py' 2026-03-06T06:54:02,659 adding 'lobster/agents/state.py' 2026-03-06T06:54:02,662 adding 'lobster/agents/supervisor.py' 2026-03-06T06:54:02,663 adding 'lobster/cli_internal/__init__.py' 2026-03-06T06:54:02,667 adding 'lobster/cli_internal/go_tui_launcher.py' 2026-03-06T06:54:02,669 adding 'lobster/cli_internal/startup_diagnostics.py' 2026-03-06T06:54:02,671 adding 'lobster/cli_internal/commands/__init__.py' 2026-03-06T06:54:02,673 adding 'lobster/cli_internal/commands/output_adapter.py' 2026-03-06T06:54:02,675 adding 'lobster/cli_internal/commands/heavy/__init__.py' 2026-03-06T06:54:02,677 adding 'lobster/cli_internal/commands/heavy/animations.py' 2026-03-06T06:54:02,682 adding 'lobster/cli_internal/commands/heavy/chat_commands.py' 2026-03-06T06:54:02,684 adding 'lobster/cli_internal/commands/heavy/data_commands.py' 2026-03-06T06:54:02,686 adding 'lobster/cli_internal/commands/heavy/display_helpers.py' 2026-03-06T06:54:02,697 adding 'lobster/cli_internal/commands/heavy/init_commands.py' 2026-03-06T06:54:02,700 adding 'lobster/cli_internal/commands/heavy/modality_commands.py' 2026-03-06T06:54:02,702 adding 'lobster/cli_internal/commands/heavy/query_commands.py' 2026-03-06T06:54:02,706 adding 'lobster/cli_internal/commands/heavy/session_infra.py' 2026-03-06T06:54:02,720 adding 'lobster/cli_internal/commands/heavy/slash_commands.py' 2026-03-06T06:54:02,723 adding 'lobster/cli_internal/commands/heavy/visualization_commands.py' 2026-03-06T06:54:02,725 adding 'lobster/cli_internal/commands/light/__init__.py' 2026-03-06T06:54:02,727 adding 'lobster/cli_internal/commands/light/agent_commands.py' 2026-03-06T06:54:02,734 adding 'lobster/cli_internal/commands/light/config_commands.py' 2026-03-06T06:54:02,738 adding 'lobster/cli_internal/commands/light/file_commands.py' 2026-03-06T06:54:02,742 adding 'lobster/cli_internal/commands/light/metadata_commands.py' 2026-03-06T06:54:02,744 adding 'lobster/cli_internal/commands/light/pipeline_commands.py' 2026-03-06T06:54:02,746 adding 'lobster/cli_internal/commands/light/purge_commands.py' 2026-03-06T06:54:02,750 adding 'lobster/cli_internal/commands/light/queue_commands.py' 2026-03-06T06:54:02,751 adding 'lobster/cli_internal/commands/light/scaffold_commands.py' 2026-03-06T06:54:02,752 adding 'lobster/cli_internal/commands/light/validate_commands.py' 2026-03-06T06:54:02,754 adding 'lobster/cli_internal/commands/light/vector_search_commands.py' 2026-03-06T06:54:02,757 adding 'lobster/cli_internal/commands/light/workspace_commands.py' 2026-03-06T06:54:02,759 adding 'lobster/cli_internal/utils/__init__.py' 2026-03-06T06:54:02,760 adding 'lobster/cli_internal/utils/path_resolution.py' 2026-03-06T06:54:02,763 adding 'lobster/config/__init__.py' 2026-03-06T06:54:02,764 adding 'lobster/config/agent_capabilities.py' 2026-03-06T06:54:02,766 adding 'lobster/config/agent_config_endpoint.py' 2026-03-06T06:54:02,768 adding 'lobster/config/agent_config_resolver.py' 2026-03-06T06:54:02,769 adding 'lobster/config/agent_defaults.py' 2026-03-06T06:54:02,770 adding 'lobster/config/agent_presets.py' 2026-03-06T06:54:02,772 adding 'lobster/config/agent_registry.py' 2026-03-06T06:54:02,774 adding 'lobster/config/aquadif.py' 2026-03-06T06:54:02,775 adding 'lobster/config/base_config.py' 2026-03-06T06:54:02,777 adding 'lobster/config/config_manager.py' 2026-03-06T06:54:02,778 adding 'lobster/config/constants.py' 2026-03-06T06:54:02,780 adding 'lobster/config/global_config.py' 2026-03-06T06:54:02,782 adding 'lobster/config/llm_factory.py' 2026-03-06T06:54:02,784 adding 'lobster/config/ollama_service.py' 2026-03-06T06:54:02,785 adding 'lobster/config/provider_setup.py' 2026-03-06T06:54:02,788 adding 'lobster/config/settings.py' 2026-03-06T06:54:02,790 adding 'lobster/config/ssl_setup.py' 2026-03-06T06:54:02,792 adding 'lobster/config/subscription_tiers.py' 2026-03-06T06:54:02,793 adding 'lobster/config/supervisor_config.py' 2026-03-06T06:54:02,795 adding 'lobster/config/version_check.py' 2026-03-06T06:54:02,797 adding 'lobster/config/workspace_agent_config.py' 2026-03-06T06:54:02,799 adding 'lobster/config/workspace_config.py' 2026-03-06T06:54:02,800 adding 'lobster/config/providers/__init__.py' 2026-03-06T06:54:02,802 adding 'lobster/config/providers/anthropic_provider.py' 2026-03-06T06:54:02,804 adding 'lobster/config/providers/azure_provider.py' 2026-03-06T06:54:02,806 adding 'lobster/config/providers/base_provider.py' 2026-03-06T06:54:02,808 adding 'lobster/config/providers/bedrock_provider.py' 2026-03-06T06:54:02,810 adding 'lobster/config/providers/gemini_provider.py' 2026-03-06T06:54:02,813 adding 'lobster/config/providers/ollama_provider.py' 2026-03-06T06:54:02,815 adding 'lobster/config/providers/openai_provider.py' 2026-03-06T06:54:02,817 adding 'lobster/config/providers/openrouter_provider.py' 2026-03-06T06:54:02,819 adding 'lobster/config/providers/registry.py' 2026-03-06T06:54:02,821 adding 'lobster/core/__init__.py' 2026-03-06T06:54:02,822 adding 'lobster/core/analysis_ir.py' 2026-03-06T06:54:02,824 adding 'lobster/core/aquadif_monitor.py' 2026-03-06T06:54:02,826 adding 'lobster/core/archive_utils.py' 2026-03-06T06:54:02,838 adding 'lobster/core/client.py' 2026-03-06T06:54:02,842 adding 'lobster/core/component_registry.py' 2026-03-06T06:54:02,845 adding 'lobster/core/config_resolver.py' 2026-03-06T06:54:02,846 adding 'lobster/core/data_manager_v2.py' 2026-03-06T06:54:02,847 adding 'lobster/core/download_queue.py' 2026-03-06T06:54:02,849 adding 'lobster/core/exceptions.py' 2026-03-06T06:54:02,851 adding 'lobster/core/extraction_cache.py' 2026-03-06T06:54:02,852 adding 'lobster/core/ir_coverage.py' 2026-03-06T06:54:02,853 adding 'lobster/core/license_manager.py' 2026-03-06T06:54:02,854 adding 'lobster/core/lineage.py' 2026-03-06T06:54:02,855 adding 'lobster/core/notebook_executor.py' 2026-03-06T06:54:02,857 adding 'lobster/core/notebook_exporter.py' 2026-03-06T06:54:02,858 adding 'lobster/core/notebook_validator.py' 2026-03-06T06:54:02,861 adding 'lobster/core/omics_registry.py' 2026-03-06T06:54:02,864 adding 'lobster/core/plot_manager.py' 2026-03-06T06:54:02,866 adding 'lobster/core/plugin_loader.py' 2026-03-06T06:54:02,867 adding 'lobster/core/protocols.py' 2026-03-06T06:54:02,868 adding 'lobster/core/publication_queue.py' 2026-03-06T06:54:02,869 adding 'lobster/core/queue_storage.py' 2026-03-06T06:54:02,872 adding 'lobster/core/ris_parser.py' 2026-03-06T06:54:02,873 adding 'lobster/core/sparse_utils.py' 2026-03-06T06:54:02,874 adding 'lobster/core/uv_tool_env.py' 2026-03-06T06:54:02,875 adding 'lobster/core/workspace.py' 2026-03-06T06:54:02,877 adding 'lobster/core/adapters/__init__.py' 2026-03-06T06:54:02,880 adding 'lobster/core/adapters/base.py' 2026-03-06T06:54:02,883 adding 'lobster/core/adapters/metabolomics_adapter.py' 2026-03-06T06:54:02,885 adding 'lobster/core/adapters/protein_structure_adapter.py' 2026-03-06T06:54:02,889 adding 'lobster/core/adapters/proteomics_adapter.py' 2026-03-06T06:54:02,891 adding 'lobster/core/adapters/pseudobulk_adapter.py' 2026-03-06T06:54:02,895 adding 'lobster/core/adapters/transcriptomics_adapter.py' 2026-03-06T06:54:02,896 adding 'lobster/core/adapters/genomics/__init__.py' 2026-03-06T06:54:02,899 adding 'lobster/core/adapters/genomics/plink_adapter.py' 2026-03-06T06:54:02,902 adding 'lobster/core/adapters/genomics/vcf_adapter.py' 2026-03-06T06:54:02,904 adding 'lobster/core/backends/__init__.py' 2026-03-06T06:54:02,905 adding 'lobster/core/backends/base.py' 2026-03-06T06:54:02,909 adding 'lobster/core/backends/h5ad_backend.py' 2026-03-06T06:54:02,911 adding 'lobster/core/backends/mudata_backend.py' 2026-03-06T06:54:02,913 adding 'lobster/core/governance/__init__.py' 2026-03-06T06:54:02,914 adding 'lobster/core/governance/aquadif_monitor.py' 2026-03-06T06:54:02,918 adding 'lobster/core/governance/license_manager.py' 2026-03-06T06:54:02,919 adding 'lobster/core/identifiers/__init__.py' 2026-03-06T06:54:02,922 adding 'lobster/core/identifiers/accession_resolver.py' 2026-03-06T06:54:02,924 adding 'lobster/core/interfaces/__init__.py' 2026-03-06T06:54:02,925 adding 'lobster/core/interfaces/adapter.py' 2026-03-06T06:54:02,927 adding 'lobster/core/interfaces/backend.py' 2026-03-06T06:54:02,928 adding 'lobster/core/interfaces/base_client.py' 2026-03-06T06:54:02,931 adding 'lobster/core/interfaces/download_service.py' 2026-03-06T06:54:02,932 adding 'lobster/core/interfaces/queue_preparer.py' 2026-03-06T06:54:02,934 adding 'lobster/core/interfaces/validator.py' 2026-03-06T06:54:02,936 adding 'lobster/core/notebooks/__init__.py' 2026-03-06T06:54:02,938 adding 'lobster/core/notebooks/executor.py' 2026-03-06T06:54:02,942 adding 'lobster/core/notebooks/exporter.py' 2026-03-06T06:54:02,944 adding 'lobster/core/notebooks/validator.py' 2026-03-06T06:54:02,945 adding 'lobster/core/provenance/__init__.py' 2026-03-06T06:54:02,948 adding 'lobster/core/provenance/analysis_ir.py' 2026-03-06T06:54:02,950 adding 'lobster/core/provenance/ir_coverage.py' 2026-03-06T06:54:02,953 adding 'lobster/core/provenance/lineage.py' 2026-03-06T06:54:02,956 adding 'lobster/core/provenance/provenance.py' 2026-03-06T06:54:02,958 adding 'lobster/core/queues/__init__.py' 2026-03-06T06:54:02,960 adding 'lobster/core/queues/download_queue.py' 2026-03-06T06:54:02,962 adding 'lobster/core/queues/publication_queue.py' 2026-03-06T06:54:02,964 adding 'lobster/core/queues/queue_storage.py' 2026-03-06T06:54:02,965 adding 'lobster/core/runtime/__init__.py' 2026-03-06T06:54:02,982 adding 'lobster/core/runtime/data_manager.py' 2026-03-06T06:54:02,984 adding 'lobster/core/runtime/workspace.py' 2026-03-06T06:54:02,986 adding 'lobster/core/schemas/__init__.py' 2026-03-06T06:54:02,988 adding 'lobster/core/schemas/clinical_schema.py' 2026-03-06T06:54:02,992 adding 'lobster/core/schemas/database_mappings.py' 2026-03-06T06:54:02,993 adding 'lobster/core/schemas/database_registry.py' 2026-03-06T06:54:02,996 adding 'lobster/core/schemas/download_queue.py' 2026-03-06T06:54:02,998 adding 'lobster/core/schemas/download_urls.py' 2026-03-06T06:54:03,003 adding 'lobster/core/schemas/export_schemas.py' 2026-03-06T06:54:03,007 adding 'lobster/core/schemas/genomics.py' 2026-03-06T06:54:03,011 adding 'lobster/core/schemas/metabolomics.py' 2026-03-06T06:54:03,016 adding 'lobster/core/schemas/metagenomics.py' 2026-03-06T06:54:03,018 adding 'lobster/core/schemas/ontology.py' 2026-03-06T06:54:03,020 adding 'lobster/core/schemas/protein_structure.py' 2026-03-06T06:54:03,023 adding 'lobster/core/schemas/proteomics.py' 2026-03-06T06:54:03,026 adding 'lobster/core/schemas/publication_queue.py' 2026-03-06T06:54:03,028 adding 'lobster/core/schemas/search.py' 2026-03-06T06:54:03,032 adding 'lobster/core/schemas/sra.py' 2026-03-06T06:54:03,039 adding 'lobster/core/schemas/transcriptomics.py' 2026-03-06T06:54:03,041 adding 'lobster/core/schemas/validation.py' 2026-03-06T06:54:03,042 adding 'lobster/core/utils/__init__.py' 2026-03-06T06:54:03,045 adding 'lobster/core/utils/h5ad_utils.py' 2026-03-06T06:54:03,047 adding 'lobster/core/vector/__init__.py' 2026-03-06T06:54:03,048 adding 'lobster/core/vector/config.py' 2026-03-06T06:54:03,050 adding 'lobster/core/vector/ontology_graph.py' 2026-03-06T06:54:03,051 adding 'lobster/core/vector/service.py' 2026-03-06T06:54:03,052 adding 'lobster/core/vector/backends/__init__.py' 2026-03-06T06:54:03,053 adding 'lobster/core/vector/backends/base.py' 2026-03-06T06:54:03,055 adding 'lobster/core/vector/backends/chromadb_backend.py' 2026-03-06T06:54:03,056 adding 'lobster/core/vector/embeddings/__init__.py' 2026-03-06T06:54:03,058 adding 'lobster/core/vector/rerankers/__init__.py' 2026-03-06T06:54:03,059 adding 'lobster/integrations/__init__.py' 2026-03-06T06:54:03,061 adding 'lobster/integrations/langchain_tui_backend.py' 2026-03-06T06:54:03,063 adding 'lobster/lobster_cloud/__init__.py' 2026-03-06T06:54:03,064 adding 'lobster/lobster_cloud/client.py' 2026-03-06T06:54:03,066 adding 'lobster/prompts/__init__.py' 2026-03-06T06:54:03,068 adding 'lobster/prompts/composer.py' 2026-03-06T06:54:03,069 adding 'lobster/prompts/config.py' 2026-03-06T06:54:03,071 adding 'lobster/prompts/loader.py' 2026-03-06T06:54:03,072 adding 'lobster/prompts/registry.py' 2026-03-06T06:54:03,074 adding 'lobster/scaffold/__init__.py' 2026-03-06T06:54:03,076 adding 'lobster/scaffold/validators.py' 2026-03-06T06:54:03,077 adding 'lobster/scaffold/generators/__init__.py' 2026-03-06T06:54:03,079 adding 'lobster/scaffold/generators/agent.py' 2026-03-06T06:54:03,081 adding 'lobster/scaffold/templates/README.md.j2' 2026-03-06T06:54:03,082 adding 'lobster/scaffold/templates/__init__.py.j2' 2026-03-06T06:54:03,084 adding 'lobster/scaffold/templates/agent.py.j2' 2026-03-06T06:54:03,085 adding 'lobster/scaffold/templates/config.py.j2' 2026-03-06T06:54:03,086 adding 'lobster/scaffold/templates/conftest.py.j2' 2026-03-06T06:54:03,087 adding 'lobster/scaffold/templates/prompts.py.j2' 2026-03-06T06:54:03,089 adding 'lobster/scaffold/templates/pyproject.toml.j2' 2026-03-06T06:54:03,090 adding 'lobster/scaffold/templates/shared_tools.py.j2' 2026-03-06T06:54:03,091 adding 'lobster/scaffold/templates/state.py.j2' 2026-03-06T06:54:03,093 adding 'lobster/scaffold/templates/test_contract.py.j2' 2026-03-06T06:54:03,102 adding 'lobster/services/analysis/bulk_rnaseq_service.py' 2026-03-06T06:54:03,113 adding 'lobster/services/analysis/clustering_service.py' 2026-03-06T06:54:03,116 adding 'lobster/services/analysis/pathway_enrichment_bridge_service.py' 2026-03-06T06:54:03,119 adding 'lobster/services/analysis/pathway_enrichment_service.py' 2026-03-06T06:54:03,127 adding 'lobster/services/data_access/content_access_service.py' 2026-03-06T06:54:03,133 adding 'lobster/services/data_access/docling_service.py' 2026-03-06T06:54:03,136 adding 'lobster/services/data_access/ensembl_service.py' 2026-03-06T06:54:03,138 adding 'lobster/services/data_access/geo_download_service.py' 2026-03-06T06:54:03,141 adding 'lobster/services/data_access/geo_fallback_service.py' 2026-03-06T06:54:03,144 adding 'lobster/services/data_access/geo_queue_preparer.py' 2026-03-06T06:54:03,145 adding 'lobster/services/data_access/geo_service.py' 2026-03-06T06:54:03,148 adding 'lobster/services/data_access/massive_download_service.py' 2026-03-06T06:54:03,149 adding 'lobster/services/data_access/massive_queue_preparer.py' 2026-03-06T06:54:03,153 adding 'lobster/services/data_access/metabolights_download_service.py' 2026-03-06T06:54:03,156 adding 'lobster/services/data_access/metabolights_queue_preparer.py' 2026-03-06T06:54:03,158 adding 'lobster/services/data_access/pride_download_service.py' 2026-03-06T06:54:03,160 adding 'lobster/services/data_access/pride_queue_preparer.py' 2026-03-06T06:54:03,161 adding 'lobster/services/data_access/queue_preparation_service.py' 2026-03-06T06:54:03,166 adding 'lobster/services/data_access/sra_download_service.py' 2026-03-06T06:54:03,168 adding 'lobster/services/data_access/sra_queue_preparer.py' 2026-03-06T06:54:03,169 adding 'lobster/services/data_access/uniprot_service.py' 2026-03-06T06:54:03,174 adding 'lobster/services/data_access/workspace_content_service.py' 2026-03-06T06:54:03,176 adding 'lobster/services/data_access/geo/__init__.py' 2026-03-06T06:54:03,180 adding 'lobster/services/data_access/geo/archive_processing.py' 2026-03-06T06:54:03,183 adding 'lobster/services/data_access/geo/concatenation.py' 2026-03-06T06:54:03,184 adding 'lobster/services/data_access/geo/constants.py' 2026-03-06T06:54:03,189 adding 'lobster/services/data_access/geo/download_execution.py' 2026-03-06T06:54:03,193 adding 'lobster/services/data_access/geo/downloader.py' 2026-03-06T06:54:03,194 adding 'lobster/services/data_access/geo/facade.py' 2026-03-06T06:54:03,196 adding 'lobster/services/data_access/geo/helpers.py' 2026-03-06T06:54:03,200 adding 'lobster/services/data_access/geo/matrix_parsing.py' 2026-03-06T06:54:03,206 adding 'lobster/services/data_access/geo/metadata_fetch.py' 2026-03-06T06:54:03,214 adding 'lobster/services/data_access/geo/parser.py' 2026-03-06T06:54:03,216 adding 'lobster/services/data_access/geo/soft_download.py' 2026-03-06T06:54:03,218 adding 'lobster/services/data_access/geo/strategy.py' 2026-03-06T06:54:03,221 adding 'lobster/services/data_access/geo/loaders/tenx.py' 2026-03-06T06:54:03,223 adding 'lobster/services/data_access/proteomics_parsers/__init__.py' 2026-03-06T06:54:03,225 adding 'lobster/services/data_access/proteomics_parsers/base_parser.py' 2026-03-06T06:54:03,227 adding 'lobster/services/data_access/proteomics_parsers/file_classifier.py' 2026-03-06T06:54:03,233 adding 'lobster/services/data_management/concatenation_service.py' 2026-03-06T06:54:03,236 adding 'lobster/services/data_management/modality_management_service.py' 2026-03-06T06:54:03,238 adding 'lobster/services/data_management/strategy_recommendation_service.py' 2026-03-06T06:54:03,243 adding 'lobster/services/execution/custom_code_execution_service.py' 2026-03-06T06:54:03,245 adding 'lobster/services/execution/execution_context_builder.py' 2026-03-06T06:54:03,246 adding 'lobster/services/execution/registry.py' 2026-03-06T06:54:03,248 adding 'lobster/services/execution/sdk_delegation_service.py' 2026-03-06T06:54:03,251 adding 'lobster/services/metadata/identifier_provenance_service.py' 2026-03-06T06:54:03,253 adding 'lobster/services/metadata/metadata_overview_service.py' 2026-03-06T06:54:03,256 adding 'lobster/services/metadata/metadata_validation_service.py' 2026-03-06T06:54:03,258 adding 'lobster/services/metadata/protocol_extraction/base.py' 2026-03-06T06:54:03,260 adding 'lobster/services/metadata/protocol_extraction/registry.py' 2026-03-06T06:54:03,262 adding 'lobster/services/metadata/protocol_extraction/amplicon/details.py' 2026-03-06T06:54:03,265 adding 'lobster/services/metadata/protocol_extraction/amplicon/service.py' 2026-03-06T06:54:03,267 adding 'lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json' 2026-03-06T06:54:03,269 adding 'lobster/services/metadata/protocol_extraction/mass_spec/details.py' 2026-03-06T06:54:03,270 adding 'lobster/services/metadata/protocol_extraction/mass_spec/service.py' 2026-03-06T06:54:03,272 adding 'lobster/services/metadata/protocol_extraction/rnaseq/details.py' 2026-03-06T06:54:03,274 adding 'lobster/services/metadata/protocol_extraction/rnaseq/service.py' 2026-03-06T06:54:03,283 adding 'lobster/services/orchestration/publication_processing_service.py' 2026-03-06T06:54:03,285 adding 'lobster/testing/__init__.py' 2026-03-06T06:54:03,288 adding 'lobster/testing/contract_mixins.py' 2026-03-06T06:54:03,290 adding 'lobster/testing/fixtures.py' 2026-03-06T06:54:03,292 adding 'lobster/testing/mock_data_manager.py' 2026-03-06T06:54:03,293 adding 'lobster/testing/mock_llm.py' 2026-03-06T06:54:03,295 adding 'lobster/tools/__init__.py' 2026-03-06T06:54:03,298 adding 'lobster/tools/custom_code_tool.py' 2026-03-06T06:54:03,300 adding 'lobster/tools/download_orchestrator.py' 2026-03-06T06:54:03,302 adding 'lobster/tools/filesystem_tools.py' 2026-03-06T06:54:03,304 adding 'lobster/tools/gpu_detector.py' 2026-03-06T06:54:03,307 adding 'lobster/tools/knowledgebase_tools.py' 2026-03-06T06:54:03,308 adding 'lobster/tools/pipeline_strategy.py' 2026-03-06T06:54:03,312 adding 'lobster/tools/rate_limiter.py' 2026-03-06T06:54:03,316 adding 'lobster/tools/rate_limiter_arena.py' 2026-03-06T06:54:03,318 adding 'lobster/tools/store_tools.py' 2026-03-06T06:54:03,319 adding 'lobster/tools/todo_tools.py' 2026-03-06T06:54:03,321 adding 'lobster/tools/url_transforms.py' 2026-03-06T06:54:03,324 adding 'lobster/tools/workflow_tracker.py' 2026-03-06T06:54:03,334 adding 'lobster/tools/workspace_tool.py' 2026-03-06T06:54:03,336 adding 'lobster/tools/providers/__init__.py' 2026-03-06T06:54:03,338 adding 'lobster/tools/providers/abstract_provider.py' 2026-03-06T06:54:03,340 adding 'lobster/tools/providers/base_provider.py' 2026-03-06T06:54:03,342 adding 'lobster/tools/providers/biopython_entrez_wrapper.py' 2026-03-06T06:54:03,344 adding 'lobster/tools/providers/biorxiv_medrxiv_config.py' 2026-03-06T06:54:03,349 adding 'lobster/tools/providers/biorxiv_medrxiv_provider.py' 2026-03-06T06:54:03,355 adding 'lobster/tools/providers/geo_provider.py' 2026-03-06T06:54:03,357 adding 'lobster/tools/providers/geo_utils.py' 2026-03-06T06:54:03,360 adding 'lobster/tools/providers/massive_provider.py' 2026-03-06T06:54:03,363 adding 'lobster/tools/providers/metabolights_provider.py' 2026-03-06T06:54:03,366 adding 'lobster/tools/providers/ncbi_query_builder.py' 2026-03-06T06:54:03,367 adding 'lobster/tools/providers/organism_enum.py' 2026-03-06T06:54:03,370 adding 'lobster/tools/providers/pdb_provider.py' 2026-03-06T06:54:03,376 adding 'lobster/tools/providers/pmc_provider.py' 2026-03-06T06:54:03,379 adding 'lobster/tools/providers/pride_normalizer.py' 2026-03-06T06:54:03,382 adding 'lobster/tools/providers/pride_provider.py' 2026-03-06T06:54:03,384 adding 'lobster/tools/providers/provider_registry.py' 2026-03-06T06:54:03,388 adding 'lobster/tools/providers/publication_resolver.py' 2026-03-06T06:54:03,396 adding 'lobster/tools/providers/pubmed_provider.py' 2026-03-06T06:54:03,403 adding 'lobster/tools/providers/sra_provider.py' 2026-03-06T06:54:03,405 adding 'lobster/tools/providers/structure_provider.py' 2026-03-06T06:54:03,407 adding 'lobster/tools/providers/webpage_provider.py' 2026-03-06T06:54:03,409 adding 'lobster/ui/__init__.py' 2026-03-06T06:54:03,411 adding 'lobster/ui/backend.py' 2026-03-06T06:54:03,414 adding 'lobster/ui/commands.py' 2026-03-06T06:54:03,416 adding 'lobster/ui/console_manager.py' 2026-03-06T06:54:03,419 adding 'lobster/ui/live_dashboard.py' 2026-03-06T06:54:03,420 adding 'lobster/ui/os_app.py' 2026-03-06T06:54:03,423 adding 'lobster/ui/progress_manager.py' 2026-03-06T06:54:03,425 adding 'lobster/ui/themes.py' 2026-03-06T06:54:03,427 adding 'lobster/ui/bridge/__init__.py' 2026-03-06T06:54:03,428 adding 'lobster/ui/bridge/binary_finder.py' 2026-03-06T06:54:03,430 adding 'lobster/ui/bridge/go_tui_bridge.py' 2026-03-06T06:54:03,432 adding 'lobster/ui/bridge/init_adapter.py' 2026-03-06T06:54:03,433 adding 'lobster/ui/bridge/protocol.py' 2026-03-06T06:54:03,435 adding 'lobster/ui/bridge/questionary_fallback.py' 2026-03-06T06:54:03,437 adding 'lobster/ui/callbacks/__init__.py' 2026-03-06T06:54:03,438 adding 'lobster/ui/callbacks/protocol_callback.py' 2026-03-06T06:54:03,441 adding 'lobster/ui/callbacks/textual_callback.py' 2026-03-06T06:54:03,443 adding 'lobster/ui/components/__init__.py' 2026-03-06T06:54:03,445 adding 'lobster/ui/components/file_tree.py' 2026-03-06T06:54:03,447 adding 'lobster/ui/components/multi_progress.py' 2026-03-06T06:54:03,449 adding 'lobster/ui/components/parallel_workers_progress.py' 2026-03-06T06:54:03,451 adding 'lobster/ui/components/status_display.py' 2026-03-06T06:54:03,453 adding 'lobster/ui/formatters/__init__.py' 2026-03-06T06:54:03,454 adding 'lobster/ui/screens/__init__.py' 2026-03-06T06:54:03,458 adding 'lobster/ui/screens/analysis_screen.py' 2026-03-06T06:54:03,460 adding 'lobster/ui/services/__init__.py' 2026-03-06T06:54:03,462 adding 'lobster/ui/services/error_service.py' 2026-03-06T06:54:03,463 adding 'lobster/ui/widgets/__init__.py' 2026-03-06T06:54:03,465 adding 'lobster/ui/widgets/activity_log.py' 2026-03-06T06:54:03,467 adding 'lobster/ui/widgets/adapters_panel.py' 2026-03-06T06:54:03,468 adding 'lobster/ui/widgets/agents_panel.py' 2026-03-06T06:54:03,469 adding 'lobster/ui/widgets/chat_message.py' 2026-03-06T06:54:03,471 adding 'lobster/ui/widgets/connections_panel.py' 2026-03-06T06:54:03,474 adding 'lobster/ui/widgets/data_hub.py' 2026-03-06T06:54:03,476 adding 'lobster/ui/widgets/error_modal.py' 2026-03-06T06:54:03,477 adding 'lobster/ui/widgets/modality_list.py' 2026-03-06T06:54:03,479 adding 'lobster/ui/widgets/plot_preview.py' 2026-03-06T06:54:03,480 adding 'lobster/ui/widgets/query_prompt.py' 2026-03-06T06:54:03,482 adding 'lobster/ui/widgets/queue_panel.py' 2026-03-06T06:54:03,483 adding 'lobster/ui/widgets/queue_status_bar.py' 2026-03-06T06:54:03,484 adding 'lobster/ui/widgets/results_display.py' 2026-03-06T06:54:03,486 adding 'lobster/ui/widgets/status_bar.py' 2026-03-06T06:54:03,488 adding 'lobster/ui/widgets/system_info.py' 2026-03-06T06:54:03,489 adding 'lobster/ui/widgets/token_usage_panel.py' 2026-03-06T06:54:03,491 adding 'lobster/utils/__init__.py' 2026-03-06T06:54:03,497 adding 'lobster/utils/callbacks.py' 2026-03-06T06:54:03,499 adding 'lobster/utils/deviance.py' 2026-03-06T06:54:03,505 adding 'lobster/utils/error_handlers.py' 2026-03-06T06:54:03,508 adding 'lobster/utils/file_analyzer.py' 2026-03-06T06:54:03,510 adding 'lobster/utils/file_naming.py' 2026-03-06T06:54:03,512 adding 'lobster/utils/gene_annotation.py' 2026-03-06T06:54:03,514 adding 'lobster/utils/json_extractor.py' 2026-03-06T06:54:03,515 adding 'lobster/utils/llm_response_utils.py' 2026-03-06T06:54:03,516 adding 'lobster/utils/logger.py' 2026-03-06T06:54:03,518 adding 'lobster/utils/progress_wrapper.py' 2026-03-06T06:54:03,520 adding 'lobster/utils/ssl_utils.py' 2026-03-06T06:54:03,521 adding 'lobster/utils/statistics.py' 2026-03-06T06:54:03,523 adding 'lobster/utils/system.py' 2026-03-06T06:54:03,530 adding 'lobster_ai-1.1.1.dist-info/licenses/LICENSE' 2026-03-06T06:54:03,532 adding 'lobster_ai-1.1.1.dist-info/METADATA' 2026-03-06T06:54:03,534 adding 'lobster_ai-1.1.1.dist-info/WHEEL' 2026-03-06T06:54:03,535 adding 'lobster_ai-1.1.1.dist-info/entry_points.txt' 2026-03-06T06:54:03,536 adding 'lobster_ai-1.1.1.dist-info/top_level.txt' 2026-03-06T06:54:03,541 adding 'lobster_ai-1.1.1.dist-info/RECORD' 2026-03-06T06:54:03,562 removing build/bdist.linux-armv7l/wheel 2026-03-06T06:54:03,751 Building wheel for lobster-ai (pyproject.toml): finished with status 'done' 2026-03-06T06:54:03,782 Created wheel for lobster-ai: filename=lobster_ai-1.1.1-py3-none-any.whl size=1463288 sha256=f58d1e37e6bde0f97da1bed96cc4805a9ae806b28a4939984cc2a66909a46939 2026-03-06T06:54:03,783 Stored in directory: /tmp/pip-ephem-wheel-cache-gpmdlidz/wheels/82/f9/ba/3271c881b2c2fd5eb9f1802b1dc71bfe15dc94a236d3a50582 2026-03-06T06:54:03,812 Successfully built lobster-ai 2026-03-06T06:54:03,860 Removed build tracker: '/tmp/pip-build-tracker-m2j5lyry'