2026-01-06T11:06:46,139 Created temporary directory: /tmp/pip-ephem-wheel-cache-m3sey1y9 2026-01-06T11:06:46,141 Created temporary directory: /tmp/pip-build-tracker-gaagxmw1 2026-01-06T11:06:46,141 Initialized build tracking at /tmp/pip-build-tracker-gaagxmw1 2026-01-06T11:06:46,142 Created build tracker: /tmp/pip-build-tracker-gaagxmw1 2026-01-06T11:06:46,142 Entered build tracker: /tmp/pip-build-tracker-gaagxmw1 2026-01-06T11:06:46,143 Created temporary directory: /tmp/pip-wheel-5guwouk8 2026-01-06T11:06:46,146 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-01-06T11:06:46,148 Created temporary directory: /tmp/pip-ephem-wheel-cache-ffmawshz 2026-01-06T11:06:46,170 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-06T11:06:46,174 2 location(s) to search for versions of lobster-ai: 2026-01-06T11:06:46,174 * https://pypi.org/simple/lobster-ai/ 2026-01-06T11:06:46,174 * https://www.piwheels.org/simple/lobster-ai/ 2026-01-06T11:06:46,175 Fetching project page and analyzing links: https://pypi.org/simple/lobster-ai/ 2026-01-06T11:06:46,176 Getting page https://pypi.org/simple/lobster-ai/ 2026-01-06T11:06:46,177 Found index url https://pypi.org/simple 2026-01-06T11:06:46,388 Fetched page https://pypi.org/simple/lobster-ai/ as application/vnd.pypi.simple.v1+json 2026-01-06T11:06:46,390 Skipping link: No binaries permitted for lobster-ai: https://files.pythonhosted.org/packages/25/73/1d1a25243200fd27fb678fc6ba25c4f1675657400551cb051e2f0ba608ec/lobster_ai-0.4.0.6-py3-none-any.whl (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11) 2026-01-06T11:06:46,391 Found link https://files.pythonhosted.org/packages/70/bb/d1a5b8fb3972b827f824ed05220013d162bbec24be0d8bffe790e535960b/lobster_ai-0.4.0.6.tar.gz (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11), version: 0.4.0.6 2026-01-06T11:06:46,392 Skipping link: No binaries permitted for lobster-ai: https://files.pythonhosted.org/packages/28/50/4706e55b526417192c7d0734f9300f26cbaa6f3404a258dc5e23932755d8/lobster_ai-0.4.0.7-py3-none-any.whl (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11) 2026-01-06T11:06:46,393 Found link https://files.pythonhosted.org/packages/a8/80/ed27ba2c77f7614bf149a697b450c4828da9d56fe5c8d3f0090165bf76fc/lobster_ai-0.4.0.7.tar.gz (from https://pypi.org/simple/lobster-ai/) (requires-python:>=3.11), version: 0.4.0.7 2026-01-06T11:06:46,394 Fetching project page and analyzing links: https://www.piwheels.org/simple/lobster-ai/ 2026-01-06T11:06:46,395 Getting page https://www.piwheels.org/simple/lobster-ai/ 2026-01-06T11:06:46,396 Found index url https://www.piwheels.org/simple 2026-01-06T11:06:46,762 Fetched page https://www.piwheels.org/simple/lobster-ai/ as text/html 2026-01-06T11:06:46,765 Skipping link: No binaries permitted for lobster-ai: https://www.piwheels.org/simple/lobster-ai/lobster_ai-0.4.0.6-py3-none-any.whl#sha256=2d937b84c8a017772656d9ca05d13ea77671ba5c8b1eccb92e4129465a975502 (from https://www.piwheels.org/simple/lobster-ai/) (requires-python:>=3.11) 2026-01-06T11:06:46,767 Skipping link: not a file: https://www.piwheels.org/simple/lobster-ai/ 2026-01-06T11:06:46,768 Skipping link: not a file: https://pypi.org/simple/lobster-ai/ 2026-01-06T11:06:46,813 Given no hashes to check 1 links for project 'lobster-ai': discarding no candidates 2026-01-06T11:06:46,855 Collecting lobster-ai==0.4.0.7 2026-01-06T11:06:46,860 Created temporary directory: /tmp/pip-unpack-ueaxw2gy 2026-01-06T11:06:46,995 Downloading lobster_ai-0.4.0.7.tar.gz (1.1 MB) 2026-01-06T11:06:47,820 Added lobster-ai==0.4.0.7 from https://files.pythonhosted.org/packages/a8/80/ed27ba2c77f7614bf149a697b450c4828da9d56fe5c8d3f0090165bf76fc/lobster_ai-0.4.0.7.tar.gz to build tracker '/tmp/pip-build-tracker-gaagxmw1' 2026-01-06T11:06:47,829 Created temporary directory: /tmp/pip-build-env-emcggey3 2026-01-06T11:06:47,834 Installing build dependencies: started 2026-01-06T11:06:47,835 Running command pip subprocess to install build dependencies 2026-01-06T11:06:48,972 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-01-06T11:06:49,626 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-01-06T11:06:49,649 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-06T11:06:51,377 Collecting setuptools>=65.0 2026-01-06T11:06:51,552 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2026-01-06T11:06:51,832 Collecting wheel 2026-01-06T11:06:51,847 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2026-01-06T11:06:54,859 Installing collected packages: wheel, setuptools 2026-01-06T11:06:55,101 Creating /tmp/pip-build-env-emcggey3/overlay/local/bin 2026-01-06T11:06:55,103 changing mode of /tmp/pip-build-env-emcggey3/overlay/local/bin/wheel to 755 2026-01-06T11:06:58,762 Successfully installed setuptools-80.9.0 wheel-0.45.1 2026-01-06T11:06:59,034 Installing build dependencies: finished with status 'done' 2026-01-06T11:06:59,041 Getting requirements to build wheel: started 2026-01-06T11:06:59,042 Running command Getting requirements to build wheel 2026-01-06T11:06:59,973 /tmp/pip-build-env-emcggey3/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml` 2026-01-06T11:06:59,973 corresp(dist, value, root_dir) 2026-01-06T11:06:59,974 /tmp/pip-build-env-emcggey3/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-01-06T11:06:59,975 corresp(dist, value, root_dir) 2026-01-06T11:06:59,975 /tmp/pip-build-env-emcggey3/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies) 2026-01-06T11:06:59,976 corresp(dist, value, root_dir) 2026-01-06T11:07:00,084 running egg_info 2026-01-06T11:07:00,091 writing lobster_ai.egg-info/PKG-INFO 2026-01-06T11:07:00,121 writing dependency_links to lobster_ai.egg-info/dependency_links.txt 2026-01-06T11:07:00,123 writing entry points to lobster_ai.egg-info/entry_points.txt 2026-01-06T11:07:00,143 writing requirements to lobster_ai.egg-info/requires.txt 2026-01-06T11:07:00,144 writing top-level names to lobster_ai.egg-info/top_level.txt 2026-01-06T11:07:00,275 reading manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-01-06T11:07:00,290 adding license file 'LICENSE' 2026-01-06T11:07:00,303 writing manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-01-06T11:07:00,403 Getting requirements to build wheel: finished with status 'done' 2026-01-06T11:07:00,407 Created temporary directory: /tmp/pip-modern-metadata-oo9pftli 2026-01-06T11:07:00,409 Preparing metadata (pyproject.toml): started 2026-01-06T11:07:00,410 Running command Preparing metadata (pyproject.toml) 2026-01-06T11:07:01,037 /tmp/pip-build-env-emcggey3/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml` 2026-01-06T11:07:01,038 corresp(dist, value, root_dir) 2026-01-06T11:07:01,038 /tmp/pip-build-env-emcggey3/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-01-06T11:07:01,039 corresp(dist, value, root_dir) 2026-01-06T11:07:01,040 /tmp/pip-build-env-emcggey3/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies) 2026-01-06T11:07:01,040 corresp(dist, value, root_dir) 2026-01-06T11:07:01,141 running dist_info 2026-01-06T11:07:01,153 creating /tmp/pip-modern-metadata-oo9pftli/lobster_ai.egg-info 2026-01-06T11:07:01,154 writing /tmp/pip-modern-metadata-oo9pftli/lobster_ai.egg-info/PKG-INFO 2026-01-06T11:07:01,185 writing dependency_links to /tmp/pip-modern-metadata-oo9pftli/lobster_ai.egg-info/dependency_links.txt 2026-01-06T11:07:01,186 writing entry points to /tmp/pip-modern-metadata-oo9pftli/lobster_ai.egg-info/entry_points.txt 2026-01-06T11:07:01,206 writing requirements to /tmp/pip-modern-metadata-oo9pftli/lobster_ai.egg-info/requires.txt 2026-01-06T11:07:01,207 writing top-level names to /tmp/pip-modern-metadata-oo9pftli/lobster_ai.egg-info/top_level.txt 2026-01-06T11:07:01,208 writing manifest file '/tmp/pip-modern-metadata-oo9pftli/lobster_ai.egg-info/SOURCES.txt' 2026-01-06T11:07:01,330 reading manifest file '/tmp/pip-modern-metadata-oo9pftli/lobster_ai.egg-info/SOURCES.txt' 2026-01-06T11:07:01,332 adding license file 'LICENSE' 2026-01-06T11:07:01,342 writing manifest file '/tmp/pip-modern-metadata-oo9pftli/lobster_ai.egg-info/SOURCES.txt' 2026-01-06T11:07:01,343 creating '/tmp/pip-modern-metadata-oo9pftli/lobster_ai-0.4.0.7.dist-info' 2026-01-06T11:07:01,474 Preparing metadata (pyproject.toml): finished with status 'done' 2026-01-06T11:07:01,482 Source in /tmp/pip-wheel-5guwouk8/lobster-ai_e57cc5370deb4f558f68220c97ed94d4 has version 0.4.0.7, which satisfies requirement lobster-ai==0.4.0.7 from https://files.pythonhosted.org/packages/a8/80/ed27ba2c77f7614bf149a697b450c4828da9d56fe5c8d3f0090165bf76fc/lobster_ai-0.4.0.7.tar.gz 2026-01-06T11:07:01,483 Removed lobster-ai==0.4.0.7 from https://files.pythonhosted.org/packages/a8/80/ed27ba2c77f7614bf149a697b450c4828da9d56fe5c8d3f0090165bf76fc/lobster_ai-0.4.0.7.tar.gz from build tracker '/tmp/pip-build-tracker-gaagxmw1' 2026-01-06T11:07:01,493 Created temporary directory: /tmp/pip-unpack-tqpvy7_j 2026-01-06T11:07:01,494 Building wheels for collected packages: lobster-ai 2026-01-06T11:07:01,498 Created temporary directory: /tmp/pip-wheel-3qauje32 2026-01-06T11:07:01,499 Destination directory: /tmp/pip-wheel-3qauje32 2026-01-06T11:07:01,501 Building wheel for lobster-ai (pyproject.toml): started 2026-01-06T11:07:01,502 Running command Building wheel for lobster-ai (pyproject.toml) 2026-01-06T11:07:02,136 /tmp/pip-build-env-emcggey3/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml` 2026-01-06T11:07:02,136 corresp(dist, value, root_dir) 2026-01-06T11:07:02,137 /tmp/pip-build-env-emcggey3/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-01-06T11:07:02,138 corresp(dist, value, root_dir) 2026-01-06T11:07:02,138 /tmp/pip-build-env-emcggey3/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies) 2026-01-06T11:07:02,139 corresp(dist, value, root_dir) 2026-01-06T11:07:02,229 running bdist_wheel 2026-01-06T11:07:02,250 running build 2026-01-06T11:07:02,250 running build_py 2026-01-06T11:07:02,257 creating build/lib/lobster 2026-01-06T11:07:02,260 copying lobster/__main__.py -> build/lib/lobster 2026-01-06T11:07:02,262 copying lobster/main.py -> build/lib/lobster 2026-01-06T11:07:02,264 copying lobster/_version.py -> build/lib/lobster 2026-01-06T11:07:02,266 copying lobster/version.py -> build/lib/lobster 2026-01-06T11:07:02,267 copying lobster/cli.py -> build/lib/lobster 2026-01-06T11:07:02,275 creating build/lib/lobster/config 2026-01-06T11:07:02,276 copying lobster/config/settings.py -> build/lib/lobster/config 2026-01-06T11:07:02,278 copying lobster/config/subscription_tiers.py -> build/lib/lobster/config 2026-01-06T11:07:02,280 copying lobster/config/__init__.py -> build/lib/lobster/config 2026-01-06T11:07:02,282 copying lobster/config/provider_setup.py -> build/lib/lobster/config 2026-01-06T11:07:02,284 copying lobster/config/agent_config.py -> build/lib/lobster/config 2026-01-06T11:07:02,287 copying lobster/config/constants.py -> build/lib/lobster/config 2026-01-06T11:07:02,289 copying lobster/config/agent_registry.py -> build/lib/lobster/config 2026-01-06T11:07:02,291 copying lobster/config/config_manager.py -> build/lib/lobster/config 2026-01-06T11:07:02,293 copying lobster/config/global_config.py -> build/lib/lobster/config 2026-01-06T11:07:02,295 copying lobster/config/workspace_config.py -> build/lib/lobster/config 2026-01-06T11:07:02,298 copying lobster/config/agent_capabilities.py -> build/lib/lobster/config 2026-01-06T11:07:02,300 copying lobster/config/supervisor_config.py -> build/lib/lobster/config 2026-01-06T11:07:02,302 copying lobster/config/base_config.py -> build/lib/lobster/config 2026-01-06T11:07:02,304 copying lobster/config/llm_factory.py -> build/lib/lobster/config 2026-01-06T11:07:02,307 creating build/lib/lobster/utils 2026-01-06T11:07:02,308 copying lobster/utils/ssl_utils.py -> build/lib/lobster/utils 2026-01-06T11:07:02,310 copying lobster/utils/file_naming.py -> build/lib/lobster/utils 2026-01-06T11:07:02,313 copying lobster/utils/__init__.py -> build/lib/lobster/utils 2026-01-06T11:07:02,315 copying lobster/utils/error_handlers.py -> build/lib/lobster/utils 2026-01-06T11:07:02,317 copying lobster/utils/progress_wrapper.py -> build/lib/lobster/utils 2026-01-06T11:07:02,319 copying lobster/utils/deviance.py -> build/lib/lobster/utils 2026-01-06T11:07:02,321 copying lobster/utils/system.py -> build/lib/lobster/utils 2026-01-06T11:07:02,323 copying lobster/utils/logger.py -> build/lib/lobster/utils 2026-01-06T11:07:02,325 copying lobster/utils/json_extractor.py -> build/lib/lobster/utils 2026-01-06T11:07:02,328 copying lobster/utils/callbacks.py -> build/lib/lobster/utils 2026-01-06T11:07:02,331 copying lobster/utils/file_analyzer.py -> build/lib/lobster/utils 2026-01-06T11:07:02,334 creating build/lib/lobster/core 2026-01-06T11:07:02,335 copying lobster/core/component_registry.py -> build/lib/lobster/core 2026-01-06T11:07:02,337 copying lobster/core/exceptions.py -> build/lib/lobster/core 2026-01-06T11:07:02,340 copying lobster/core/notebook_exporter.py -> build/lib/lobster/core 2026-01-06T11:07:02,343 copying lobster/core/data_manager_v2.py -> build/lib/lobster/core 2026-01-06T11:07:02,347 copying lobster/core/ris_parser.py -> build/lib/lobster/core 2026-01-06T11:07:02,349 copying lobster/core/__init__.py -> build/lib/lobster/core 2026-01-06T11:07:02,351 copying lobster/core/provenance.py -> build/lib/lobster/core 2026-01-06T11:07:02,354 copying lobster/core/publication_queue.py -> build/lib/lobster/core 2026-01-06T11:07:02,356 copying lobster/core/workspace.py -> build/lib/lobster/core 2026-01-06T11:07:02,358 copying lobster/core/download_queue.py -> build/lib/lobster/core 2026-01-06T11:07:02,361 copying lobster/core/config_resolver.py -> build/lib/lobster/core 2026-01-06T11:07:02,363 copying lobster/core/notebook_executor.py -> build/lib/lobster/core 2026-01-06T11:07:02,365 copying lobster/core/plugin_loader.py -> build/lib/lobster/core 2026-01-06T11:07:02,368 copying lobster/core/client.py -> build/lib/lobster/core 2026-01-06T11:07:02,372 copying lobster/core/archive_utils.py -> build/lib/lobster/core 2026-01-06T11:07:02,374 copying lobster/core/plot_manager.py -> build/lib/lobster/core 2026-01-06T11:07:02,377 copying lobster/core/license_manager.py -> build/lib/lobster/core 2026-01-06T11:07:02,380 copying lobster/core/queue_storage.py -> build/lib/lobster/core 2026-01-06T11:07:02,382 copying lobster/core/notebook_validator.py -> build/lib/lobster/core 2026-01-06T11:07:02,384 copying lobster/core/ir_coverage.py -> build/lib/lobster/core 2026-01-06T11:07:02,386 copying lobster/core/analysis_ir.py -> build/lib/lobster/core 2026-01-06T11:07:02,389 creating build/lib/lobster/lobster_cloud 2026-01-06T11:07:02,390 copying lobster/lobster_cloud/__init__.py -> build/lib/lobster/lobster_cloud 2026-01-06T11:07:02,392 copying lobster/lobster_cloud/client.py -> build/lib/lobster/lobster_cloud 2026-01-06T11:07:02,396 creating build/lib/lobster/services 2026-01-06T11:07:02,397 copying lobster/services/__init__.py -> build/lib/lobster/services 2026-01-06T11:07:02,399 creating build/lib/lobster/agents 2026-01-06T11:07:02,400 copying lobster/agents/__init__.py -> build/lib/lobster/agents 2026-01-06T11:07:02,401 copying lobster/agents/data_expert.py -> build/lib/lobster/agents 2026-01-06T11:07:02,404 copying lobster/agents/draw_graph.py -> build/lib/lobster/agents 2026-01-06T11:07:02,406 copying lobster/agents/visualization_expert.py -> build/lib/lobster/agents 2026-01-06T11:07:02,409 copying lobster/agents/data_expert_assistant.py -> build/lib/lobster/agents 2026-01-06T11:07:02,412 copying lobster/agents/supervisor.py -> build/lib/lobster/agents 2026-01-06T11:07:02,415 copying lobster/agents/graph.py -> build/lib/lobster/agents 2026-01-06T11:07:02,417 copying lobster/agents/state.py -> build/lib/lobster/agents 2026-01-06T11:07:02,420 copying lobster/agents/research_agent.py -> build/lib/lobster/agents 2026-01-06T11:07:02,424 creating build/lib/lobster/cli_internal 2026-01-06T11:07:02,425 copying lobster/cli_internal/__init__.py -> build/lib/lobster/cli_internal 2026-01-06T11:07:02,428 creating build/lib/lobster/ui 2026-01-06T11:07:02,429 copying lobster/ui/__init__.py -> build/lib/lobster/ui 2026-01-06T11:07:02,431 copying lobster/ui/live_dashboard.py -> build/lib/lobster/ui 2026-01-06T11:07:02,433 copying lobster/ui/progress_manager.py -> build/lib/lobster/ui 2026-01-06T11:07:02,436 copying lobster/ui/console_manager.py -> build/lib/lobster/ui 2026-01-06T11:07:02,438 copying lobster/ui/themes.py -> build/lib/lobster/ui 2026-01-06T11:07:02,441 creating build/lib/lobster/tools 2026-01-06T11:07:02,442 copying lobster/tools/geo_downloader.py -> build/lib/lobster/tools 2026-01-06T11:07:02,444 copying lobster/tools/enhanced_handoff_tool.py -> build/lib/lobster/tools 2026-01-06T11:07:02,447 copying lobster/tools/__init__.py -> build/lib/lobster/tools 2026-01-06T11:07:02,448 copying lobster/tools/workspace_tool.py -> build/lib/lobster/tools 2026-01-06T11:07:02,452 copying lobster/tools/pipeline_strategy.py -> build/lib/lobster/tools 2026-01-06T11:07:02,454 copying lobster/tools/handoff_tool.py -> build/lib/lobster/tools 2026-01-06T11:07:02,456 copying lobster/tools/download_orchestrator.py -> build/lib/lobster/tools 2026-01-06T11:07:02,459 copying lobster/tools/geo_parser.py -> build/lib/lobster/tools 2026-01-06T11:07:02,461 copying lobster/tools/gpu_detector.py -> build/lib/lobster/tools 2026-01-06T11:07:02,463 copying lobster/tools/rate_limiter.py -> build/lib/lobster/tools 2026-01-06T11:07:02,465 copying lobster/tools/todo_tools.py -> build/lib/lobster/tools 2026-01-06T11:07:02,468 copying lobster/tools/url_transforms.py -> build/lib/lobster/tools 2026-01-06T11:07:02,470 copying lobster/tools/expert_handoff_patterns.py -> build/lib/lobster/tools 2026-01-06T11:07:02,472 copying lobster/tools/expert_handoff_manager.py -> build/lib/lobster/tools 2026-01-06T11:07:02,474 copying lobster/tools/workflow_tracker.py -> build/lib/lobster/tools 2026-01-06T11:07:02,477 copying lobster/tools/custom_code_tool.py -> build/lib/lobster/tools 2026-01-06T11:07:02,480 creating build/lib/lobster/config/providers 2026-01-06T11:07:02,481 copying lobster/config/providers/base_provider.py -> build/lib/lobster/config/providers 2026-01-06T11:07:02,483 copying lobster/config/providers/gemini_provider.py -> build/lib/lobster/config/providers 2026-01-06T11:07:02,486 copying lobster/config/providers/__init__.py -> build/lib/lobster/config/providers 2026-01-06T11:07:02,488 copying lobster/config/providers/bedrock_provider.py -> build/lib/lobster/config/providers 2026-01-06T11:07:02,490 copying lobster/config/providers/anthropic_provider.py -> build/lib/lobster/config/providers 2026-01-06T11:07:02,492 copying lobster/config/providers/ollama_provider.py -> build/lib/lobster/config/providers 2026-01-06T11:07:02,495 copying lobster/config/providers/registry.py -> build/lib/lobster/config/providers 2026-01-06T11:07:02,497 creating build/lib/lobster/core/interfaces 2026-01-06T11:07:02,498 copying lobster/core/interfaces/__init__.py -> build/lib/lobster/core/interfaces 2026-01-06T11:07:02,500 copying lobster/core/interfaces/adapter.py -> build/lib/lobster/core/interfaces 2026-01-06T11:07:02,502 copying lobster/core/interfaces/download_service.py -> build/lib/lobster/core/interfaces 2026-01-06T11:07:02,505 copying lobster/core/interfaces/backend.py -> build/lib/lobster/core/interfaces 2026-01-06T11:07:02,507 copying lobster/core/interfaces/base_client.py -> build/lib/lobster/core/interfaces 2026-01-06T11:07:02,509 copying lobster/core/interfaces/validator.py -> build/lib/lobster/core/interfaces 2026-01-06T11:07:02,512 creating build/lib/lobster/core/adapters 2026-01-06T11:07:02,513 copying lobster/core/adapters/base.py -> build/lib/lobster/core/adapters 2026-01-06T11:07:02,516 copying lobster/core/adapters/__init__.py -> build/lib/lobster/core/adapters 2026-01-06T11:07:02,517 copying lobster/core/adapters/transcriptomics_adapter.py -> build/lib/lobster/core/adapters 2026-01-06T11:07:02,520 copying lobster/core/adapters/proteomics_adapter.py -> build/lib/lobster/core/adapters 2026-01-06T11:07:02,522 copying lobster/core/adapters/protein_structure_adapter.py -> build/lib/lobster/core/adapters 2026-01-06T11:07:02,525 copying lobster/core/adapters/pseudobulk_adapter.py -> build/lib/lobster/core/adapters 2026-01-06T11:07:02,528 creating build/lib/lobster/core/utils 2026-01-06T11:07:02,529 copying lobster/core/utils/__init__.py -> build/lib/lobster/core/utils 2026-01-06T11:07:02,531 copying lobster/core/utils/h5ad_utils.py -> build/lib/lobster/core/utils 2026-01-06T11:07:02,534 creating build/lib/lobster/core/backends 2026-01-06T11:07:02,536 copying lobster/core/backends/base.py -> build/lib/lobster/core/backends 2026-01-06T11:07:02,539 copying lobster/core/backends/__init__.py -> build/lib/lobster/core/backends 2026-01-06T11:07:02,541 copying lobster/core/backends/mudata_backend.py -> build/lib/lobster/core/backends 2026-01-06T11:07:02,543 copying lobster/core/backends/h5ad_backend.py -> build/lib/lobster/core/backends 2026-01-06T11:07:02,546 creating build/lib/lobster/core/identifiers 2026-01-06T11:07:02,548 copying lobster/core/identifiers/__init__.py -> build/lib/lobster/core/identifiers 2026-01-06T11:07:02,550 copying lobster/core/identifiers/accession_resolver.py -> build/lib/lobster/core/identifiers 2026-01-06T11:07:02,553 creating build/lib/lobster/core/schemas 2026-01-06T11:07:02,554 copying lobster/core/schemas/database_registry.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,557 copying lobster/core/schemas/sra.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,559 copying lobster/core/schemas/export_schemas.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,562 copying lobster/core/schemas/__init__.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,564 copying lobster/core/schemas/database_mappings.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,567 copying lobster/core/schemas/protein_structure.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,569 copying lobster/core/schemas/publication_queue.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,572 copying lobster/core/schemas/transcriptomics.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,575 copying lobster/core/schemas/proteomics.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,578 copying lobster/core/schemas/download_queue.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,580 copying lobster/core/schemas/validation.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,583 copying lobster/core/schemas/metagenomics.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,586 copying lobster/core/schemas/metabolomics.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,589 copying lobster/core/schemas/download_urls.py -> build/lib/lobster/core/schemas 2026-01-06T11:07:02,592 creating build/lib/lobster/services/templates 2026-01-06T11:07:02,593 copying lobster/services/templates/__init__.py -> build/lib/lobster/services/templates 2026-01-06T11:07:02,594 copying lobster/services/templates/annotation_templates.py -> build/lib/lobster/services/templates 2026-01-06T11:07:02,598 creating build/lib/lobster/services/visualization 2026-01-06T11:07:02,599 copying lobster/services/visualization/pymol_visualization_service.py -> build/lib/lobster/services/visualization 2026-01-06T11:07:02,602 copying lobster/services/visualization/visualization_service.py -> build/lib/lobster/services/visualization 2026-01-06T11:07:02,606 copying lobster/services/visualization/__init__.py -> build/lib/lobster/services/visualization 2026-01-06T11:07:02,607 copying lobster/services/visualization/bulk_visualization_service.py -> build/lib/lobster/services/visualization 2026-01-06T11:07:02,610 creating build/lib/lobster/services/metadata 2026-01-06T11:07:02,611 copying lobster/services/metadata/identifier_provenance_service.py -> build/lib/lobster/services/metadata 2026-01-06T11:07:02,614 copying lobster/services/metadata/metadata_validation_service.py -> build/lib/lobster/services/metadata 2026-01-06T11:07:02,616 copying lobster/services/metadata/metadata_standardization_service.py -> build/lib/lobster/services/metadata 2026-01-06T11:07:02,619 copying lobster/services/metadata/__init__.py -> build/lib/lobster/services/metadata 2026-01-06T11:07:02,621 copying lobster/services/metadata/manual_annotation_service.py -> build/lib/lobster/services/metadata 2026-01-06T11:07:02,624 copying lobster/services/metadata/sample_grouping_service.py -> build/lib/lobster/services/metadata 2026-01-06T11:07:02,627 creating build/lib/lobster/services/quality 2026-01-06T11:07:02,628 copying lobster/services/quality/__init__.py -> build/lib/lobster/services/quality 2026-01-06T11:07:02,630 copying lobster/services/quality/preprocessing_service.py -> build/lib/lobster/services/quality 2026-01-06T11:07:02,633 copying lobster/services/quality/quality_service.py -> build/lib/lobster/services/quality 2026-01-06T11:07:02,637 creating build/lib/lobster/services/ml 2026-01-06T11:07:02,638 copying lobster/services/ml/__init__.py -> build/lib/lobster/services/ml 2026-01-06T11:07:02,640 creating build/lib/lobster/services/data_management 2026-01-06T11:07:02,641 copying lobster/services/data_management/concatenation_service.py -> build/lib/lobster/services/data_management 2026-01-06T11:07:02,645 copying lobster/services/data_management/__init__.py -> build/lib/lobster/services/data_management 2026-01-06T11:07:02,646 copying lobster/services/data_management/modality_management_service.py -> build/lib/lobster/services/data_management 2026-01-06T11:07:02,649 creating build/lib/lobster/services/orchestration 2026-01-06T11:07:02,650 copying lobster/services/orchestration/publication_processing_service.py -> build/lib/lobster/services/orchestration 2026-01-06T11:07:02,654 copying lobster/services/orchestration/__init__.py -> build/lib/lobster/services/orchestration 2026-01-06T11:07:02,657 creating build/lib/lobster/services/analysis 2026-01-06T11:07:02,658 copying lobster/services/analysis/structure_analysis_service.py -> build/lib/lobster/services/analysis 2026-01-06T11:07:02,661 copying lobster/services/analysis/pseudobulk_service.py -> build/lib/lobster/services/analysis 2026-01-06T11:07:02,663 copying lobster/services/analysis/enhanced_singlecell_service.py -> build/lib/lobster/services/analysis 2026-01-06T11:07:02,666 copying lobster/services/analysis/__init__.py -> build/lib/lobster/services/analysis 2026-01-06T11:07:02,668 copying lobster/services/analysis/bulk_rnaseq_service.py -> build/lib/lobster/services/analysis 2026-01-06T11:07:02,672 copying lobster/services/analysis/differential_formula_service.py -> build/lib/lobster/services/analysis 2026-01-06T11:07:02,675 copying lobster/services/analysis/scvi_embedding_service.py -> build/lib/lobster/services/analysis 2026-01-06T11:07:02,677 copying lobster/services/analysis/clustering_service.py -> build/lib/lobster/services/analysis 2026-01-06T11:07:02,682 creating build/lib/lobster/services/execution 2026-01-06T11:07:02,683 copying lobster/services/execution/custom_code_execution_service.py -> build/lib/lobster/services/execution 2026-01-06T11:07:02,686 copying lobster/services/execution/__init__.py -> build/lib/lobster/services/execution 2026-01-06T11:07:02,688 copying lobster/services/execution/execution_context_builder.py -> build/lib/lobster/services/execution 2026-01-06T11:07:02,690 creating build/lib/lobster/services/data_access 2026-01-06T11:07:02,691 copying lobster/services/data_access/content_access_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,696 copying lobster/services/data_access/protein_structure_fetch_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,698 copying lobster/services/data_access/geo_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,708 copying lobster/services/data_access/sra_download_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,711 copying lobster/services/data_access/pride_download_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,714 copying lobster/services/data_access/geo_fallback_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,717 copying lobster/services/data_access/__init__.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,719 copying lobster/services/data_access/docling_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,723 copying lobster/services/data_access/workspace_content_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,726 copying lobster/services/data_access/geo_download_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,728 copying lobster/services/data_access/massive_download_service.py -> build/lib/lobster/services/data_access 2026-01-06T11:07:02,731 creating build/lib/lobster/services/metadata/protocol_extraction 2026-01-06T11:07:02,733 copying lobster/services/metadata/protocol_extraction/base.py -> build/lib/lobster/services/metadata/protocol_extraction 2026-01-06T11:07:02,735 copying lobster/services/metadata/protocol_extraction/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction 2026-01-06T11:07:02,737 creating build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-01-06T11:07:02,738 copying lobster/services/metadata/protocol_extraction/amplicon/service.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-01-06T11:07:02,741 copying lobster/services/metadata/protocol_extraction/amplicon/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-01-06T11:07:02,743 copying lobster/services/metadata/protocol_extraction/amplicon/details.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-01-06T11:07:02,746 creating build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-06T11:07:02,747 copying lobster/services/metadata/protocol_extraction/rnaseq/service.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-06T11:07:02,749 copying lobster/services/metadata/protocol_extraction/rnaseq/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-06T11:07:02,751 copying lobster/services/metadata/protocol_extraction/rnaseq/details.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-06T11:07:02,754 creating build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-06T11:07:02,755 copying lobster/services/metadata/protocol_extraction/mass_spec/service.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-06T11:07:02,757 copying lobster/services/metadata/protocol_extraction/mass_spec/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-06T11:07:02,759 copying lobster/services/metadata/protocol_extraction/mass_spec/details.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-06T11:07:02,762 creating build/lib/lobster/services/data_access/geo 2026-01-06T11:07:02,763 copying lobster/services/data_access/geo/strategy.py -> build/lib/lobster/services/data_access/geo 2026-01-06T11:07:02,765 copying lobster/services/data_access/geo/__init__.py -> build/lib/lobster/services/data_access/geo 2026-01-06T11:07:02,767 copying lobster/services/data_access/geo/facade.py -> build/lib/lobster/services/data_access/geo 2026-01-06T11:07:02,769 copying lobster/services/data_access/geo/downloader.py -> build/lib/lobster/services/data_access/geo 2026-01-06T11:07:02,772 copying lobster/services/data_access/geo/constants.py -> build/lib/lobster/services/data_access/geo 2026-01-06T11:07:02,774 copying lobster/services/data_access/geo/parser.py -> build/lib/lobster/services/data_access/geo 2026-01-06T11:07:02,778 creating build/lib/lobster/services/data_access/geo/metadata 2026-01-06T11:07:02,779 copying lobster/services/data_access/geo/metadata/__init__.py -> build/lib/lobster/services/data_access/geo/metadata 2026-01-06T11:07:02,781 creating build/lib/lobster/services/data_access/geo/sample 2026-01-06T11:07:02,782 copying lobster/services/data_access/geo/sample/__init__.py -> build/lib/lobster/services/data_access/geo/sample 2026-01-06T11:07:02,785 creating build/lib/lobster/services/data_access/geo/utils 2026-01-06T11:07:02,786 copying lobster/services/data_access/geo/utils/__init__.py -> build/lib/lobster/services/data_access/geo/utils 2026-01-06T11:07:02,788 creating build/lib/lobster/services/data_access/geo/loaders 2026-01-06T11:07:02,789 copying lobster/services/data_access/geo/loaders/__init__.py -> build/lib/lobster/services/data_access/geo/loaders 2026-01-06T11:07:02,791 copying lobster/services/data_access/geo/loaders/tenx.py -> build/lib/lobster/services/data_access/geo/loaders 2026-01-06T11:07:02,794 creating build/lib/lobster/agents/archive 2026-01-06T11:07:02,795 copying lobster/agents/archive/research_agent_assistant.py -> build/lib/lobster/agents/archive 2026-01-06T11:07:02,798 creating build/lib/lobster/agents/proteomics 2026-01-06T11:07:02,799 copying lobster/agents/proteomics/__init__.py -> build/lib/lobster/agents/proteomics 2026-01-06T11:07:02,801 copying lobster/agents/proteomics/state.py -> build/lib/lobster/agents/proteomics 2026-01-06T11:07:02,803 creating build/lib/lobster/agents/transcriptomics 2026-01-06T11:07:02,804 copying lobster/agents/transcriptomics/shared_tools.py -> build/lib/lobster/agents/transcriptomics 2026-01-06T11:07:02,807 copying lobster/agents/transcriptomics/__init__.py -> build/lib/lobster/agents/transcriptomics 2026-01-06T11:07:02,809 copying lobster/agents/transcriptomics/de_analysis_expert.py -> build/lib/lobster/agents/transcriptomics 2026-01-06T11:07:02,812 copying lobster/agents/transcriptomics/transcriptomics_expert.py -> build/lib/lobster/agents/transcriptomics 2026-01-06T11:07:02,816 copying lobster/agents/transcriptomics/annotation_expert.py -> build/lib/lobster/agents/transcriptomics 2026-01-06T11:07:02,819 copying lobster/agents/transcriptomics/state.py -> build/lib/lobster/agents/transcriptomics 2026-01-06T11:07:02,821 creating build/lib/lobster/agents/langgraph_supervisor 2026-01-06T11:07:02,822 copying lobster/agents/langgraph_supervisor/agent_name.py -> build/lib/lobster/agents/langgraph_supervisor 2026-01-06T11:07:02,825 copying lobster/agents/langgraph_supervisor/__init__.py -> build/lib/lobster/agents/langgraph_supervisor 2026-01-06T11:07:02,827 copying lobster/agents/langgraph_supervisor/handoff.py -> build/lib/lobster/agents/langgraph_supervisor 2026-01-06T11:07:02,829 copying lobster/agents/langgraph_supervisor/supervisor.py -> build/lib/lobster/agents/langgraph_supervisor 2026-01-06T11:07:02,832 creating build/lib/lobster/cli_internal/utils 2026-01-06T11:07:02,833 copying lobster/cli_internal/utils/__init__.py -> build/lib/lobster/cli_internal/utils 2026-01-06T11:07:02,835 copying lobster/cli_internal/utils/path_resolution.py -> build/lib/lobster/cli_internal/utils 2026-01-06T11:07:02,838 creating build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,838 copying lobster/cli_internal/commands/config_commands.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,841 copying lobster/cli_internal/commands/__init__.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,843 copying lobster/cli_internal/commands/output_adapter.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,845 copying lobster/cli_internal/commands/visualization_commands.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,848 copying lobster/cli_internal/commands/modality_commands.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,850 copying lobster/cli_internal/commands/pipeline_commands.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,852 copying lobster/cli_internal/commands/data_commands.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,855 copying lobster/cli_internal/commands/workspace_commands.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,857 copying lobster/cli_internal/commands/file_commands.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,860 copying lobster/cli_internal/commands/queue_commands.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,862 copying lobster/cli_internal/commands/metadata_commands.py -> build/lib/lobster/cli_internal/commands 2026-01-06T11:07:02,866 creating build/lib/lobster/ui/components 2026-01-06T11:07:02,866 copying lobster/ui/components/__init__.py -> build/lib/lobster/ui/components 2026-01-06T11:07:02,868 copying lobster/ui/components/multi_progress.py -> build/lib/lobster/ui/components 2026-01-06T11:07:02,871 copying lobster/ui/components/status_display.py -> build/lib/lobster/ui/components 2026-01-06T11:07:02,874 copying lobster/ui/components/file_tree.py -> build/lib/lobster/ui/components 2026-01-06T11:07:02,876 copying lobster/ui/components/parallel_workers_progress.py -> build/lib/lobster/ui/components 2026-01-06T11:07:02,879 creating build/lib/lobster/ui/formatters 2026-01-06T11:07:02,881 copying lobster/ui/formatters/__init__.py -> build/lib/lobster/ui/formatters 2026-01-06T11:07:02,884 creating build/lib/lobster/tools/archive 2026-01-06T11:07:02,885 copying lobster/tools/archive/unified_content_service.py -> build/lib/lobster/tools/archive 2026-01-06T11:07:02,888 copying lobster/tools/archive/publication_service.py -> build/lib/lobster/tools/archive 2026-01-06T11:07:02,892 creating build/lib/lobster/tools/providers 2026-01-06T11:07:02,893 copying lobster/tools/providers/structure_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,896 copying lobster/tools/providers/base_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,899 copying lobster/tools/providers/pmc_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,903 copying lobster/tools/providers/webpage_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,906 copying lobster/tools/providers/__init__.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,908 copying lobster/tools/providers/organism_enum.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,911 copying lobster/tools/providers/abstract_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,913 copying lobster/tools/providers/massive_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,916 copying lobster/tools/providers/provider_registry.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,919 copying lobster/tools/providers/pdb_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,922 copying lobster/tools/providers/pride_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,925 copying lobster/tools/providers/geo_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,930 copying lobster/tools/providers/biorxiv_medrxiv_config.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,932 copying lobster/tools/providers/sra_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,937 copying lobster/tools/providers/biorxiv_medrxiv_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,941 copying lobster/tools/providers/ncbi_query_builder.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,943 copying lobster/tools/providers/publication_resolver.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,946 copying lobster/tools/providers/pubmed_provider.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,951 copying lobster/tools/providers/geo_utils.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,953 copying lobster/tools/providers/pride_normalizer.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,956 copying lobster/tools/providers/biopython_entrez_wrapper.py -> build/lib/lobster/tools/providers 2026-01-06T11:07:02,958 running egg_info 2026-01-06T11:07:02,971 writing lobster_ai.egg-info/PKG-INFO 2026-01-06T11:07:03,002 writing dependency_links to lobster_ai.egg-info/dependency_links.txt 2026-01-06T11:07:03,004 writing entry points to lobster_ai.egg-info/entry_points.txt 2026-01-06T11:07:03,023 writing requirements to lobster_ai.egg-info/requires.txt 2026-01-06T11:07:03,024 writing top-level names to lobster_ai.egg-info/top_level.txt 2026-01-06T11:07:03,131 reading manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-01-06T11:07:03,145 adding license file 'LICENSE' 2026-01-06T11:07:03,159 writing manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-01-06T11:07:03,240 creating build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources 2026-01-06T11:07:03,241 copying lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json -> build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources 2026-01-06T11:07:03,276 installing to build/bdist.linux-armv7l/wheel 2026-01-06T11:07:03,277 running install 2026-01-06T11:07:03,300 running install_lib 2026-01-06T11:07:03,307 creating build/bdist.linux-armv7l/wheel 2026-01-06T11:07:03,309 creating build/bdist.linux-armv7l/wheel/lobster 2026-01-06T11:07:03,310 creating build/bdist.linux-armv7l/wheel/lobster/config 2026-01-06T11:07:03,312 copying build/lib/lobster/config/settings.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,314 copying build/lib/lobster/config/subscription_tiers.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,317 copying build/lib/lobster/config/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,319 copying build/lib/lobster/config/provider_setup.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,322 copying build/lib/lobster/config/agent_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,324 copying build/lib/lobster/config/constants.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,327 creating build/bdist.linux-armv7l/wheel/lobster/config/providers 2026-01-06T11:07:03,328 copying build/lib/lobster/config/providers/base_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-06T11:07:03,330 copying build/lib/lobster/config/providers/gemini_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-06T11:07:03,333 copying build/lib/lobster/config/providers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-06T11:07:03,335 copying build/lib/lobster/config/providers/bedrock_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-06T11:07:03,337 copying build/lib/lobster/config/providers/anthropic_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-06T11:07:03,339 copying build/lib/lobster/config/providers/ollama_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-06T11:07:03,342 copying build/lib/lobster/config/providers/registry.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-06T11:07:03,344 copying build/lib/lobster/config/agent_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,347 copying build/lib/lobster/config/config_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,352 copying build/lib/lobster/config/global_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,355 copying build/lib/lobster/config/workspace_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,357 copying build/lib/lobster/config/agent_capabilities.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,360 copying build/lib/lobster/config/supervisor_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,362 copying build/lib/lobster/config/base_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,364 copying build/lib/lobster/config/llm_factory.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-06T11:07:03,367 copying build/lib/lobster/__main__.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-06T11:07:03,368 copying build/lib/lobster/main.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-06T11:07:03,371 creating build/bdist.linux-armv7l/wheel/lobster/utils 2026-01-06T11:07:03,372 copying build/lib/lobster/utils/ssl_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,374 copying build/lib/lobster/utils/file_naming.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,377 copying build/lib/lobster/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,379 copying build/lib/lobster/utils/error_handlers.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,381 copying build/lib/lobster/utils/progress_wrapper.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,384 copying build/lib/lobster/utils/deviance.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,386 copying build/lib/lobster/utils/system.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,388 copying build/lib/lobster/utils/logger.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,390 copying build/lib/lobster/utils/json_extractor.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,392 copying build/lib/lobster/utils/callbacks.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,395 copying build/lib/lobster/utils/file_analyzer.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-06T11:07:03,398 copying build/lib/lobster/_version.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-06T11:07:03,401 creating build/bdist.linux-armv7l/wheel/lobster/core 2026-01-06T11:07:03,402 copying build/lib/lobster/core/component_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,405 copying build/lib/lobster/core/exceptions.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,408 creating build/bdist.linux-armv7l/wheel/lobster/core/interfaces 2026-01-06T11:07:03,410 copying build/lib/lobster/core/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-06T11:07:03,412 copying build/lib/lobster/core/interfaces/adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-06T11:07:03,414 copying build/lib/lobster/core/interfaces/download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-06T11:07:03,417 copying build/lib/lobster/core/interfaces/backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-06T11:07:03,419 copying build/lib/lobster/core/interfaces/base_client.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-06T11:07:03,421 copying build/lib/lobster/core/interfaces/validator.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-06T11:07:03,424 copying build/lib/lobster/core/notebook_exporter.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,426 copying build/lib/lobster/core/data_manager_v2.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,430 copying build/lib/lobster/core/ris_parser.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,433 copying build/lib/lobster/core/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,435 copying build/lib/lobster/core/provenance.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,437 copying build/lib/lobster/core/publication_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,440 copying build/lib/lobster/core/workspace.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,442 creating build/bdist.linux-armv7l/wheel/lobster/core/adapters 2026-01-06T11:07:03,443 copying build/lib/lobster/core/adapters/base.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-06T11:07:03,446 copying build/lib/lobster/core/adapters/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-06T11:07:03,448 copying build/lib/lobster/core/adapters/transcriptomics_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-06T11:07:03,450 copying build/lib/lobster/core/adapters/proteomics_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-06T11:07:03,454 copying build/lib/lobster/core/adapters/protein_structure_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-06T11:07:03,456 copying build/lib/lobster/core/adapters/pseudobulk_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-06T11:07:03,460 creating build/bdist.linux-armv7l/wheel/lobster/core/utils 2026-01-06T11:07:03,461 copying build/lib/lobster/core/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/utils 2026-01-06T11:07:03,463 copying build/lib/lobster/core/utils/h5ad_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/core/utils 2026-01-06T11:07:03,465 copying build/lib/lobster/core/download_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,468 copying build/lib/lobster/core/config_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,471 creating build/bdist.linux-armv7l/wheel/lobster/core/backends 2026-01-06T11:07:03,472 copying build/lib/lobster/core/backends/base.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-01-06T11:07:03,474 copying build/lib/lobster/core/backends/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-01-06T11:07:03,476 copying build/lib/lobster/core/backends/mudata_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-01-06T11:07:03,479 copying build/lib/lobster/core/backends/h5ad_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-01-06T11:07:03,482 copying build/lib/lobster/core/notebook_executor.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,485 copying build/lib/lobster/core/plugin_loader.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,488 copying build/lib/lobster/core/client.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,493 creating build/bdist.linux-armv7l/wheel/lobster/core/identifiers 2026-01-06T11:07:03,494 copying build/lib/lobster/core/identifiers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/identifiers 2026-01-06T11:07:03,496 copying build/lib/lobster/core/identifiers/accession_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/core/identifiers 2026-01-06T11:07:03,499 copying build/lib/lobster/core/archive_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,502 copying build/lib/lobster/core/plot_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,505 creating build/bdist.linux-armv7l/wheel/lobster/core/schemas 2026-01-06T11:07:03,506 copying build/lib/lobster/core/schemas/database_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,508 copying build/lib/lobster/core/schemas/sra.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,511 copying build/lib/lobster/core/schemas/export_schemas.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,514 copying build/lib/lobster/core/schemas/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,516 copying build/lib/lobster/core/schemas/database_mappings.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,519 copying build/lib/lobster/core/schemas/protein_structure.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,521 copying build/lib/lobster/core/schemas/publication_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,524 copying build/lib/lobster/core/schemas/transcriptomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,527 copying build/lib/lobster/core/schemas/proteomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,530 copying build/lib/lobster/core/schemas/download_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,533 copying build/lib/lobster/core/schemas/validation.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,535 copying build/lib/lobster/core/schemas/metagenomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,539 copying build/lib/lobster/core/schemas/metabolomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,544 copying build/lib/lobster/core/schemas/download_urls.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-06T11:07:03,547 copying build/lib/lobster/core/license_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,550 copying build/lib/lobster/core/queue_storage.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,552 copying build/lib/lobster/core/notebook_validator.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,554 copying build/lib/lobster/core/ir_coverage.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,557 copying build/lib/lobster/core/analysis_ir.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-06T11:07:03,560 creating build/bdist.linux-armv7l/wheel/lobster/lobster_cloud 2026-01-06T11:07:03,561 copying build/lib/lobster/lobster_cloud/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/lobster_cloud 2026-01-06T11:07:03,563 copying build/lib/lobster/lobster_cloud/client.py -> build/bdist.linux-armv7l/wheel/./lobster/lobster_cloud 2026-01-06T11:07:03,565 copying build/lib/lobster/version.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-06T11:07:03,567 copying build/lib/lobster/cli.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-06T11:07:03,573 creating build/bdist.linux-armv7l/wheel/lobster/services 2026-01-06T11:07:03,575 creating build/bdist.linux-armv7l/wheel/lobster/services/templates 2026-01-06T11:07:03,576 copying build/lib/lobster/services/templates/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/templates 2026-01-06T11:07:03,578 copying build/lib/lobster/services/templates/annotation_templates.py -> build/bdist.linux-armv7l/wheel/./lobster/services/templates 2026-01-06T11:07:03,582 creating build/bdist.linux-armv7l/wheel/lobster/services/visualization 2026-01-06T11:07:03,583 copying build/lib/lobster/services/visualization/pymol_visualization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization 2026-01-06T11:07:03,586 copying build/lib/lobster/services/visualization/visualization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization 2026-01-06T11:07:03,590 copying build/lib/lobster/services/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization 2026-01-06T11:07:03,592 copying build/lib/lobster/services/visualization/bulk_visualization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization 2026-01-06T11:07:03,595 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata 2026-01-06T11:07:03,596 copying build/lib/lobster/services/metadata/identifier_provenance_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-06T11:07:03,598 copying build/lib/lobster/services/metadata/metadata_validation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-06T11:07:03,601 copying build/lib/lobster/services/metadata/metadata_standardization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-06T11:07:03,604 copying build/lib/lobster/services/metadata/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-06T11:07:03,606 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction 2026-01-06T11:07:03,607 copying build/lib/lobster/services/metadata/protocol_extraction/base.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction 2026-01-06T11:07:03,609 copying build/lib/lobster/services/metadata/protocol_extraction/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction 2026-01-06T11:07:03,612 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/amplicon 2026-01-06T11:07:03,613 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon 2026-01-06T11:07:03,616 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon 2026-01-06T11:07:03,618 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/amplicon/resources 2026-01-06T11:07:03,619 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon/resources 2026-01-06T11:07:03,621 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon 2026-01-06T11:07:03,624 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-06T11:07:03,625 copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq 2026-01-06T11:07:03,628 copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq 2026-01-06T11:07:03,631 copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq 2026-01-06T11:07:03,633 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-06T11:07:03,634 copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec 2026-01-06T11:07:03,636 copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec 2026-01-06T11:07:03,638 copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec 2026-01-06T11:07:03,640 copying build/lib/lobster/services/metadata/manual_annotation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-06T11:07:03,643 copying build/lib/lobster/services/metadata/sample_grouping_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-06T11:07:03,645 copying build/lib/lobster/services/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services 2026-01-06T11:07:03,647 creating build/bdist.linux-armv7l/wheel/lobster/services/quality 2026-01-06T11:07:03,648 copying build/lib/lobster/services/quality/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/quality 2026-01-06T11:07:03,650 copying build/lib/lobster/services/quality/preprocessing_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/quality 2026-01-06T11:07:03,653 copying build/lib/lobster/services/quality/quality_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/quality 2026-01-06T11:07:03,657 creating build/bdist.linux-armv7l/wheel/lobster/services/ml 2026-01-06T11:07:03,658 copying build/lib/lobster/services/ml/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/ml 2026-01-06T11:07:03,660 creating build/bdist.linux-armv7l/wheel/lobster/services/data_management 2026-01-06T11:07:03,662 copying build/lib/lobster/services/data_management/concatenation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-01-06T11:07:03,665 copying build/lib/lobster/services/data_management/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-01-06T11:07:03,667 copying build/lib/lobster/services/data_management/modality_management_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-01-06T11:07:03,670 creating build/bdist.linux-armv7l/wheel/lobster/services/orchestration 2026-01-06T11:07:03,671 copying build/lib/lobster/services/orchestration/publication_processing_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/orchestration 2026-01-06T11:07:03,675 copying build/lib/lobster/services/orchestration/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/orchestration 2026-01-06T11:07:03,678 creating build/bdist.linux-armv7l/wheel/lobster/services/analysis 2026-01-06T11:07:03,679 copying build/lib/lobster/services/analysis/structure_analysis_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-06T11:07:03,681 copying build/lib/lobster/services/analysis/pseudobulk_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-06T11:07:03,684 copying build/lib/lobster/services/analysis/enhanced_singlecell_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-06T11:07:03,688 copying build/lib/lobster/services/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-06T11:07:03,689 copying build/lib/lobster/services/analysis/bulk_rnaseq_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-06T11:07:03,694 copying build/lib/lobster/services/analysis/differential_formula_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-06T11:07:03,697 copying build/lib/lobster/services/analysis/scvi_embedding_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-06T11:07:03,700 copying build/lib/lobster/services/analysis/clustering_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-06T11:07:03,704 creating build/bdist.linux-armv7l/wheel/lobster/services/execution 2026-01-06T11:07:03,705 copying build/lib/lobster/services/execution/custom_code_execution_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-01-06T11:07:03,709 copying build/lib/lobster/services/execution/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-01-06T11:07:03,711 copying build/lib/lobster/services/execution/execution_context_builder.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-01-06T11:07:03,714 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access 2026-01-06T11:07:03,715 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo 2026-01-06T11:07:03,717 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/metadata 2026-01-06T11:07:03,718 copying build/lib/lobster/services/data_access/geo/metadata/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/metadata 2026-01-06T11:07:03,720 copying build/lib/lobster/services/data_access/geo/strategy.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-06T11:07:03,722 copying build/lib/lobster/services/data_access/geo/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-06T11:07:03,724 copying build/lib/lobster/services/data_access/geo/facade.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-06T11:07:03,726 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/sample 2026-01-06T11:07:03,727 copying build/lib/lobster/services/data_access/geo/sample/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/sample 2026-01-06T11:07:03,730 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/utils 2026-01-06T11:07:03,731 copying build/lib/lobster/services/data_access/geo/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/utils 2026-01-06T11:07:03,733 copying build/lib/lobster/services/data_access/geo/downloader.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-06T11:07:03,736 copying build/lib/lobster/services/data_access/geo/constants.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-06T11:07:03,739 copying build/lib/lobster/services/data_access/geo/parser.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-06T11:07:03,746 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/loaders 2026-01-06T11:07:03,747 copying build/lib/lobster/services/data_access/geo/loaders/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/loaders 2026-01-06T11:07:03,751 copying build/lib/lobster/services/data_access/geo/loaders/tenx.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/loaders 2026-01-06T11:07:03,754 copying build/lib/lobster/services/data_access/content_access_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,758 copying build/lib/lobster/services/data_access/protein_structure_fetch_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,761 copying build/lib/lobster/services/data_access/geo_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,769 copying build/lib/lobster/services/data_access/sra_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,772 copying build/lib/lobster/services/data_access/pride_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,774 copying build/lib/lobster/services/data_access/geo_fallback_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,777 copying build/lib/lobster/services/data_access/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,779 copying build/lib/lobster/services/data_access/docling_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,782 copying build/lib/lobster/services/data_access/workspace_content_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,785 copying build/lib/lobster/services/data_access/geo_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,788 copying build/lib/lobster/services/data_access/massive_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-06T11:07:03,791 creating build/bdist.linux-armv7l/wheel/lobster/agents 2026-01-06T11:07:03,793 creating build/bdist.linux-armv7l/wheel/lobster/agents/archive 2026-01-06T11:07:03,794 copying build/lib/lobster/agents/archive/research_agent_assistant.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/archive 2026-01-06T11:07:03,797 copying build/lib/lobster/agents/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-06T11:07:03,798 copying build/lib/lobster/agents/data_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-06T11:07:03,802 copying build/lib/lobster/agents/draw_graph.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-06T11:07:03,804 creating build/bdist.linux-armv7l/wheel/lobster/agents/proteomics 2026-01-06T11:07:03,805 copying build/lib/lobster/agents/proteomics/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/proteomics 2026-01-06T11:07:03,807 copying build/lib/lobster/agents/proteomics/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/proteomics 2026-01-06T11:07:03,809 creating build/bdist.linux-armv7l/wheel/lobster/agents/transcriptomics 2026-01-06T11:07:03,810 copying build/lib/lobster/agents/transcriptomics/shared_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-06T11:07:03,813 copying build/lib/lobster/agents/transcriptomics/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-06T11:07:03,815 copying build/lib/lobster/agents/transcriptomics/de_analysis_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-06T11:07:03,819 copying build/lib/lobster/agents/transcriptomics/transcriptomics_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-06T11:07:03,822 copying build/lib/lobster/agents/transcriptomics/annotation_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-06T11:07:03,825 copying build/lib/lobster/agents/transcriptomics/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-06T11:07:03,827 copying build/lib/lobster/agents/visualization_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-06T11:07:03,830 copying build/lib/lobster/agents/data_expert_assistant.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-06T11:07:03,832 copying build/lib/lobster/agents/supervisor.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-06T11:07:03,835 copying build/lib/lobster/agents/graph.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-06T11:07:03,838 copying build/lib/lobster/agents/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-06T11:07:03,843 creating build/bdist.linux-armv7l/wheel/lobster/agents/langgraph_supervisor 2026-01-06T11:07:03,844 copying build/lib/lobster/agents/langgraph_supervisor/agent_name.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor 2026-01-06T11:07:03,846 copying build/lib/lobster/agents/langgraph_supervisor/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor 2026-01-06T11:07:03,848 copying build/lib/lobster/agents/langgraph_supervisor/handoff.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor 2026-01-06T11:07:03,850 copying build/lib/lobster/agents/langgraph_supervisor/supervisor.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor 2026-01-06T11:07:03,852 copying build/lib/lobster/agents/research_agent.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-06T11:07:03,857 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal 2026-01-06T11:07:03,858 copying build/lib/lobster/cli_internal/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal 2026-01-06T11:07:03,860 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/utils 2026-01-06T11:07:03,861 copying build/lib/lobster/cli_internal/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/utils 2026-01-06T11:07:03,863 copying build/lib/lobster/cli_internal/utils/path_resolution.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/utils 2026-01-06T11:07:03,866 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands 2026-01-06T11:07:03,867 copying build/lib/lobster/cli_internal/commands/config_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,870 copying build/lib/lobster/cli_internal/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,872 copying build/lib/lobster/cli_internal/commands/output_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,874 copying build/lib/lobster/cli_internal/commands/visualization_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,876 copying build/lib/lobster/cli_internal/commands/modality_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,879 copying build/lib/lobster/cli_internal/commands/pipeline_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,881 copying build/lib/lobster/cli_internal/commands/data_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,884 copying build/lib/lobster/cli_internal/commands/workspace_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,887 copying build/lib/lobster/cli_internal/commands/file_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,889 copying build/lib/lobster/cli_internal/commands/queue_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,893 copying build/lib/lobster/cli_internal/commands/metadata_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-06T11:07:03,896 creating build/bdist.linux-armv7l/wheel/lobster/ui 2026-01-06T11:07:03,897 creating build/bdist.linux-armv7l/wheel/lobster/ui/components 2026-01-06T11:07:03,898 copying build/lib/lobster/ui/components/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-06T11:07:03,900 copying build/lib/lobster/ui/components/multi_progress.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-06T11:07:03,903 copying build/lib/lobster/ui/components/status_display.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-06T11:07:03,906 copying build/lib/lobster/ui/components/file_tree.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-06T11:07:03,909 copying build/lib/lobster/ui/components/parallel_workers_progress.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-06T11:07:03,911 copying build/lib/lobster/ui/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-06T11:07:03,913 copying build/lib/lobster/ui/live_dashboard.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-06T11:07:03,916 copying build/lib/lobster/ui/progress_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-06T11:07:03,919 creating build/bdist.linux-armv7l/wheel/lobster/ui/formatters 2026-01-06T11:07:03,921 copying build/lib/lobster/ui/formatters/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/formatters 2026-01-06T11:07:03,922 copying build/lib/lobster/ui/console_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-06T11:07:03,925 copying build/lib/lobster/ui/themes.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-06T11:07:03,928 creating build/bdist.linux-armv7l/wheel/lobster/tools 2026-01-06T11:07:03,929 creating build/bdist.linux-armv7l/wheel/lobster/tools/archive 2026-01-06T11:07:03,931 copying build/lib/lobster/tools/archive/unified_content_service.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/archive 2026-01-06T11:07:03,933 copying build/lib/lobster/tools/archive/publication_service.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/archive 2026-01-06T11:07:03,936 copying build/lib/lobster/tools/geo_downloader.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:03,938 copying build/lib/lobster/tools/enhanced_handoff_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:03,941 copying build/lib/lobster/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:03,943 copying build/lib/lobster/tools/workspace_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:03,947 copying build/lib/lobster/tools/pipeline_strategy.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:03,949 copying build/lib/lobster/tools/handoff_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:03,951 copying build/lib/lobster/tools/download_orchestrator.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:03,953 copying build/lib/lobster/tools/geo_parser.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:03,955 creating build/bdist.linux-armv7l/wheel/lobster/tools/providers 2026-01-06T11:07:03,956 copying build/lib/lobster/tools/providers/structure_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,959 copying build/lib/lobster/tools/providers/base_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,961 copying build/lib/lobster/tools/providers/pmc_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,964 copying build/lib/lobster/tools/providers/webpage_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,967 copying build/lib/lobster/tools/providers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,969 copying build/lib/lobster/tools/providers/organism_enum.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,972 copying build/lib/lobster/tools/providers/abstract_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,975 copying build/lib/lobster/tools/providers/massive_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,977 copying build/lib/lobster/tools/providers/provider_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,980 copying build/lib/lobster/tools/providers/pdb_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,983 copying build/lib/lobster/tools/providers/pride_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,986 copying build/lib/lobster/tools/providers/geo_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,990 copying build/lib/lobster/tools/providers/biorxiv_medrxiv_config.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,992 copying build/lib/lobster/tools/providers/sra_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,996 copying build/lib/lobster/tools/providers/biorxiv_medrxiv_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:03,999 copying build/lib/lobster/tools/providers/ncbi_query_builder.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:04,002 copying build/lib/lobster/tools/providers/publication_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:04,006 copying build/lib/lobster/tools/providers/pubmed_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:04,011 copying build/lib/lobster/tools/providers/geo_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:04,013 copying build/lib/lobster/tools/providers/pride_normalizer.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:04,016 copying build/lib/lobster/tools/providers/biopython_entrez_wrapper.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-06T11:07:04,019 copying build/lib/lobster/tools/gpu_detector.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:04,022 copying build/lib/lobster/tools/rate_limiter.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:04,025 copying build/lib/lobster/tools/todo_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:04,028 copying build/lib/lobster/tools/url_transforms.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:04,030 copying build/lib/lobster/tools/expert_handoff_patterns.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:04,033 copying build/lib/lobster/tools/expert_handoff_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:04,035 copying build/lib/lobster/tools/workflow_tracker.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:04,039 copying build/lib/lobster/tools/custom_code_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-06T11:07:04,042 running install_egg_info 2026-01-06T11:07:04,048 Copying lobster_ai.egg-info to build/bdist.linux-armv7l/wheel/./lobster_ai-0.4.0.7-py3.11.egg-info 2026-01-06T11:07:04,064 running install_scripts 2026-01-06T11:07:04,082 creating build/bdist.linux-armv7l/wheel/lobster_ai-0.4.0.7.dist-info/WHEEL 2026-01-06T11:07:04,086 creating '/tmp/pip-wheel-3qauje32/.tmp-butkvwuf/lobster_ai-0.4.0.7-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-01-06T11:07:04,090 adding 'lobster/__main__.py' 2026-01-06T11:07:04,092 adding 'lobster/_version.py' 2026-01-06T11:07:04,136 adding 'lobster/cli.py' 2026-01-06T11:07:04,141 adding 'lobster/main.py' 2026-01-06T11:07:04,143 adding 'lobster/version.py' 2026-01-06T11:07:04,147 adding 'lobster/agents/__init__.py' 2026-01-06T11:07:04,158 adding 'lobster/agents/data_expert.py' 2026-01-06T11:07:04,163 adding 'lobster/agents/data_expert_assistant.py' 2026-01-06T11:07:04,165 adding 'lobster/agents/draw_graph.py' 2026-01-06T11:07:04,168 adding 'lobster/agents/graph.py' 2026-01-06T11:07:04,182 adding 'lobster/agents/research_agent.py' 2026-01-06T11:07:04,186 adding 'lobster/agents/state.py' 2026-01-06T11:07:04,191 adding 'lobster/agents/supervisor.py' 2026-01-06T11:07:04,194 adding 'lobster/agents/visualization_expert.py' 2026-01-06T11:07:04,198 adding 'lobster/agents/archive/research_agent_assistant.py' 2026-01-06T11:07:04,200 adding 'lobster/agents/langgraph_supervisor/__init__.py' 2026-01-06T11:07:04,202 adding 'lobster/agents/langgraph_supervisor/agent_name.py' 2026-01-06T11:07:04,204 adding 'lobster/agents/langgraph_supervisor/handoff.py' 2026-01-06T11:07:04,207 adding 'lobster/agents/langgraph_supervisor/supervisor.py' 2026-01-06T11:07:04,209 adding 'lobster/agents/proteomics/__init__.py' 2026-01-06T11:07:04,211 adding 'lobster/agents/proteomics/state.py' 2026-01-06T11:07:04,213 adding 'lobster/agents/transcriptomics/__init__.py' 2026-01-06T11:07:04,218 adding 'lobster/agents/transcriptomics/annotation_expert.py' 2026-01-06T11:07:04,227 adding 'lobster/agents/transcriptomics/de_analysis_expert.py' 2026-01-06T11:07:04,231 adding 'lobster/agents/transcriptomics/shared_tools.py' 2026-01-06T11:07:04,232 adding 'lobster/agents/transcriptomics/state.py' 2026-01-06T11:07:04,237 adding 'lobster/agents/transcriptomics/transcriptomics_expert.py' 2026-01-06T11:07:04,239 adding 'lobster/cli_internal/__init__.py' 2026-01-06T11:07:04,241 adding 'lobster/cli_internal/commands/__init__.py' 2026-01-06T11:07:04,243 adding 'lobster/cli_internal/commands/config_commands.py' 2026-01-06T11:07:04,244 adding 'lobster/cli_internal/commands/data_commands.py' 2026-01-06T11:07:04,247 adding 'lobster/cli_internal/commands/file_commands.py' 2026-01-06T11:07:04,249 adding 'lobster/cli_internal/commands/metadata_commands.py' 2026-01-06T11:07:04,252 adding 'lobster/cli_internal/commands/modality_commands.py' 2026-01-06T11:07:04,254 adding 'lobster/cli_internal/commands/output_adapter.py' 2026-01-06T11:07:04,255 adding 'lobster/cli_internal/commands/pipeline_commands.py' 2026-01-06T11:07:04,258 adding 'lobster/cli_internal/commands/queue_commands.py' 2026-01-06T11:07:04,260 adding 'lobster/cli_internal/commands/visualization_commands.py' 2026-01-06T11:07:04,263 adding 'lobster/cli_internal/commands/workspace_commands.py' 2026-01-06T11:07:04,264 adding 'lobster/cli_internal/utils/__init__.py' 2026-01-06T11:07:04,266 adding 'lobster/cli_internal/utils/path_resolution.py' 2026-01-06T11:07:04,268 adding 'lobster/config/__init__.py' 2026-01-06T11:07:04,270 adding 'lobster/config/agent_capabilities.py' 2026-01-06T11:07:04,272 adding 'lobster/config/agent_config.py' 2026-01-06T11:07:04,274 adding 'lobster/config/agent_registry.py' 2026-01-06T11:07:04,276 adding 'lobster/config/base_config.py' 2026-01-06T11:07:04,278 adding 'lobster/config/config_manager.py' 2026-01-06T11:07:04,279 adding 'lobster/config/constants.py' 2026-01-06T11:07:04,281 adding 'lobster/config/global_config.py' 2026-01-06T11:07:04,282 adding 'lobster/config/llm_factory.py' 2026-01-06T11:07:04,284 adding 'lobster/config/provider_setup.py' 2026-01-06T11:07:04,286 adding 'lobster/config/settings.py' 2026-01-06T11:07:04,288 adding 'lobster/config/subscription_tiers.py' 2026-01-06T11:07:04,289 adding 'lobster/config/supervisor_config.py' 2026-01-06T11:07:04,291 adding 'lobster/config/workspace_config.py' 2026-01-06T11:07:04,293 adding 'lobster/config/providers/__init__.py' 2026-01-06T11:07:04,295 adding 'lobster/config/providers/anthropic_provider.py' 2026-01-06T11:07:04,296 adding 'lobster/config/providers/base_provider.py' 2026-01-06T11:07:04,298 adding 'lobster/config/providers/bedrock_provider.py' 2026-01-06T11:07:04,300 adding 'lobster/config/providers/gemini_provider.py' 2026-01-06T11:07:04,303 adding 'lobster/config/providers/ollama_provider.py' 2026-01-06T11:07:04,304 adding 'lobster/config/providers/registry.py' 2026-01-06T11:07:04,307 adding 'lobster/core/__init__.py' 2026-01-06T11:07:04,309 adding 'lobster/core/analysis_ir.py' 2026-01-06T11:07:04,312 adding 'lobster/core/archive_utils.py' 2026-01-06T11:07:04,322 adding 'lobster/core/client.py' 2026-01-06T11:07:04,324 adding 'lobster/core/component_registry.py' 2026-01-06T11:07:04,326 adding 'lobster/core/config_resolver.py' 2026-01-06T11:07:04,338 adding 'lobster/core/data_manager_v2.py' 2026-01-06T11:07:04,341 adding 'lobster/core/download_queue.py' 2026-01-06T11:07:04,343 adding 'lobster/core/exceptions.py' 2026-01-06T11:07:04,345 adding 'lobster/core/ir_coverage.py' 2026-01-06T11:07:04,348 adding 'lobster/core/license_manager.py' 2026-01-06T11:07:04,350 adding 'lobster/core/notebook_executor.py' 2026-01-06T11:07:04,354 adding 'lobster/core/notebook_exporter.py' 2026-01-06T11:07:04,356 adding 'lobster/core/notebook_validator.py' 2026-01-06T11:07:04,359 adding 'lobster/core/plot_manager.py' 2026-01-06T11:07:04,361 adding 'lobster/core/plugin_loader.py' 2026-01-06T11:07:04,363 adding 'lobster/core/provenance.py' 2026-01-06T11:07:04,365 adding 'lobster/core/publication_queue.py' 2026-01-06T11:07:04,367 adding 'lobster/core/queue_storage.py' 2026-01-06T11:07:04,369 adding 'lobster/core/ris_parser.py' 2026-01-06T11:07:04,371 adding 'lobster/core/workspace.py' 2026-01-06T11:07:04,372 adding 'lobster/core/adapters/__init__.py' 2026-01-06T11:07:04,375 adding 'lobster/core/adapters/base.py' 2026-01-06T11:07:04,377 adding 'lobster/core/adapters/protein_structure_adapter.py' 2026-01-06T11:07:04,380 adding 'lobster/core/adapters/proteomics_adapter.py' 2026-01-06T11:07:04,383 adding 'lobster/core/adapters/pseudobulk_adapter.py' 2026-01-06T11:07:04,386 adding 'lobster/core/adapters/transcriptomics_adapter.py' 2026-01-06T11:07:04,388 adding 'lobster/core/backends/__init__.py' 2026-01-06T11:07:04,389 adding 'lobster/core/backends/base.py' 2026-01-06T11:07:04,393 adding 'lobster/core/backends/h5ad_backend.py' 2026-01-06T11:07:04,396 adding 'lobster/core/backends/mudata_backend.py' 2026-01-06T11:07:04,397 adding 'lobster/core/identifiers/__init__.py' 2026-01-06T11:07:04,400 adding 'lobster/core/identifiers/accession_resolver.py' 2026-01-06T11:07:04,402 adding 'lobster/core/interfaces/__init__.py' 2026-01-06T11:07:04,403 adding 'lobster/core/interfaces/adapter.py' 2026-01-06T11:07:04,405 adding 'lobster/core/interfaces/backend.py' 2026-01-06T11:07:04,406 adding 'lobster/core/interfaces/base_client.py' 2026-01-06T11:07:04,408 adding 'lobster/core/interfaces/download_service.py' 2026-01-06T11:07:04,410 adding 'lobster/core/interfaces/validator.py' 2026-01-06T11:07:04,412 adding 'lobster/core/schemas/__init__.py' 2026-01-06T11:07:04,415 adding 'lobster/core/schemas/database_mappings.py' 2026-01-06T11:07:04,417 adding 'lobster/core/schemas/database_registry.py' 2026-01-06T11:07:04,419 adding 'lobster/core/schemas/download_queue.py' 2026-01-06T11:07:04,421 adding 'lobster/core/schemas/download_urls.py' 2026-01-06T11:07:04,426 adding 'lobster/core/schemas/export_schemas.py' 2026-01-06T11:07:04,430 adding 'lobster/core/schemas/metabolomics.py' 2026-01-06T11:07:04,436 adding 'lobster/core/schemas/metagenomics.py' 2026-01-06T11:07:04,439 adding 'lobster/core/schemas/protein_structure.py' 2026-01-06T11:07:04,442 adding 'lobster/core/schemas/proteomics.py' 2026-01-06T11:07:04,445 adding 'lobster/core/schemas/publication_queue.py' 2026-01-06T11:07:04,450 adding 'lobster/core/schemas/sra.py' 2026-01-06T11:07:04,457 adding 'lobster/core/schemas/transcriptomics.py' 2026-01-06T11:07:04,459 adding 'lobster/core/schemas/validation.py' 2026-01-06T11:07:04,461 adding 'lobster/core/utils/__init__.py' 2026-01-06T11:07:04,463 adding 'lobster/core/utils/h5ad_utils.py' 2026-01-06T11:07:04,465 adding 'lobster/lobster_cloud/__init__.py' 2026-01-06T11:07:04,467 adding 'lobster/lobster_cloud/client.py' 2026-01-06T11:07:04,469 adding 'lobster/services/__init__.py' 2026-01-06T11:07:04,470 adding 'lobster/services/analysis/__init__.py' 2026-01-06T11:07:04,478 adding 'lobster/services/analysis/bulk_rnaseq_service.py' 2026-01-06T11:07:04,487 adding 'lobster/services/analysis/clustering_service.py' 2026-01-06T11:07:04,492 adding 'lobster/services/analysis/differential_formula_service.py' 2026-01-06T11:07:04,498 adding 'lobster/services/analysis/enhanced_singlecell_service.py' 2026-01-06T11:07:04,501 adding 'lobster/services/analysis/pseudobulk_service.py' 2026-01-06T11:07:04,503 adding 'lobster/services/analysis/scvi_embedding_service.py' 2026-01-06T11:07:04,506 adding 'lobster/services/analysis/structure_analysis_service.py' 2026-01-06T11:07:04,508 adding 'lobster/services/data_access/__init__.py' 2026-01-06T11:07:04,516 adding 'lobster/services/data_access/content_access_service.py' 2026-01-06T11:07:04,522 adding 'lobster/services/data_access/docling_service.py' 2026-01-06T11:07:04,525 adding 'lobster/services/data_access/geo_download_service.py' 2026-01-06T11:07:04,528 adding 'lobster/services/data_access/geo_fallback_service.py' 2026-01-06T11:07:04,552 adding 'lobster/services/data_access/geo_service.py' 2026-01-06T11:07:04,556 adding 'lobster/services/data_access/massive_download_service.py' 2026-01-06T11:07:04,558 adding 'lobster/services/data_access/pride_download_service.py' 2026-01-06T11:07:04,560 adding 'lobster/services/data_access/protein_structure_fetch_service.py' 2026-01-06T11:07:04,565 adding 'lobster/services/data_access/sra_download_service.py' 2026-01-06T11:07:04,570 adding 'lobster/services/data_access/workspace_content_service.py' 2026-01-06T11:07:04,572 adding 'lobster/services/data_access/geo/__init__.py' 2026-01-06T11:07:04,573 adding 'lobster/services/data_access/geo/constants.py' 2026-01-06T11:07:04,577 adding 'lobster/services/data_access/geo/downloader.py' 2026-01-06T11:07:04,578 adding 'lobster/services/data_access/geo/facade.py' 2026-01-06T11:07:04,585 adding 'lobster/services/data_access/geo/parser.py' 2026-01-06T11:07:04,588 adding 'lobster/services/data_access/geo/strategy.py' 2026-01-06T11:07:04,590 adding 'lobster/services/data_access/geo/loaders/__init__.py' 2026-01-06T11:07:04,592 adding 'lobster/services/data_access/geo/loaders/tenx.py' 2026-01-06T11:07:04,593 adding 'lobster/services/data_access/geo/metadata/__init__.py' 2026-01-06T11:07:04,595 adding 'lobster/services/data_access/geo/sample/__init__.py' 2026-01-06T11:07:04,596 adding 'lobster/services/data_access/geo/utils/__init__.py' 2026-01-06T11:07:04,598 adding 'lobster/services/data_management/__init__.py' 2026-01-06T11:07:04,603 adding 'lobster/services/data_management/concatenation_service.py' 2026-01-06T11:07:04,606 adding 'lobster/services/data_management/modality_management_service.py' 2026-01-06T11:07:04,607 adding 'lobster/services/execution/__init__.py' 2026-01-06T11:07:04,611 adding 'lobster/services/execution/custom_code_execution_service.py' 2026-01-06T11:07:04,613 adding 'lobster/services/execution/execution_context_builder.py' 2026-01-06T11:07:04,615 adding 'lobster/services/metadata/__init__.py' 2026-01-06T11:07:04,617 adding 'lobster/services/metadata/identifier_provenance_service.py' 2026-01-06T11:07:04,621 adding 'lobster/services/metadata/manual_annotation_service.py' 2026-01-06T11:07:04,624 adding 'lobster/services/metadata/metadata_standardization_service.py' 2026-01-06T11:07:04,627 adding 'lobster/services/metadata/metadata_validation_service.py' 2026-01-06T11:07:04,629 adding 'lobster/services/metadata/sample_grouping_service.py' 2026-01-06T11:07:04,631 adding 'lobster/services/metadata/protocol_extraction/__init__.py' 2026-01-06T11:07:04,633 adding 'lobster/services/metadata/protocol_extraction/base.py' 2026-01-06T11:07:04,634 adding 'lobster/services/metadata/protocol_extraction/amplicon/__init__.py' 2026-01-06T11:07:04,636 adding 'lobster/services/metadata/protocol_extraction/amplicon/details.py' 2026-01-06T11:07:04,639 adding 'lobster/services/metadata/protocol_extraction/amplicon/service.py' 2026-01-06T11:07:04,641 adding 'lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json' 2026-01-06T11:07:04,643 adding 'lobster/services/metadata/protocol_extraction/mass_spec/__init__.py' 2026-01-06T11:07:04,644 adding 'lobster/services/metadata/protocol_extraction/mass_spec/details.py' 2026-01-06T11:07:04,646 adding 'lobster/services/metadata/protocol_extraction/mass_spec/service.py' 2026-01-06T11:07:04,647 adding 'lobster/services/metadata/protocol_extraction/rnaseq/__init__.py' 2026-01-06T11:07:04,649 adding 'lobster/services/metadata/protocol_extraction/rnaseq/details.py' 2026-01-06T11:07:04,650 adding 'lobster/services/metadata/protocol_extraction/rnaseq/service.py' 2026-01-06T11:07:04,652 adding 'lobster/services/ml/__init__.py' 2026-01-06T11:07:04,653 adding 'lobster/services/orchestration/__init__.py' 2026-01-06T11:07:04,662 adding 'lobster/services/orchestration/publication_processing_service.py' 2026-01-06T11:07:04,663 adding 'lobster/services/quality/__init__.py' 2026-01-06T11:07:04,668 adding 'lobster/services/quality/preprocessing_service.py' 2026-01-06T11:07:04,672 adding 'lobster/services/quality/quality_service.py' 2026-01-06T11:07:04,674 adding 'lobster/services/templates/__init__.py' 2026-01-06T11:07:04,678 adding 'lobster/services/templates/annotation_templates.py' 2026-01-06T11:07:04,680 adding 'lobster/services/visualization/__init__.py' 2026-01-06T11:07:04,683 adding 'lobster/services/visualization/bulk_visualization_service.py' 2026-01-06T11:07:04,686 adding 'lobster/services/visualization/pymol_visualization_service.py' 2026-01-06T11:07:04,693 adding 'lobster/services/visualization/visualization_service.py' 2026-01-06T11:07:04,696 adding 'lobster/tools/__init__.py' 2026-01-06T11:07:04,698 adding 'lobster/tools/custom_code_tool.py' 2026-01-06T11:07:04,700 adding 'lobster/tools/download_orchestrator.py' 2026-01-06T11:07:04,702 adding 'lobster/tools/enhanced_handoff_tool.py' 2026-01-06T11:07:04,704 adding 'lobster/tools/expert_handoff_manager.py' 2026-01-06T11:07:04,706 adding 'lobster/tools/expert_handoff_patterns.py' 2026-01-06T11:07:04,707 adding 'lobster/tools/geo_downloader.py' 2026-01-06T11:07:04,709 adding 'lobster/tools/geo_parser.py' 2026-01-06T11:07:04,710 adding 'lobster/tools/gpu_detector.py' 2026-01-06T11:07:04,712 adding 'lobster/tools/handoff_tool.py' 2026-01-06T11:07:04,713 adding 'lobster/tools/pipeline_strategy.py' 2026-01-06T11:07:04,717 adding 'lobster/tools/rate_limiter.py' 2026-01-06T11:07:04,719 adding 'lobster/tools/todo_tools.py' 2026-01-06T11:07:04,720 adding 'lobster/tools/url_transforms.py' 2026-01-06T11:07:04,723 adding 'lobster/tools/workflow_tracker.py' 2026-01-06T11:07:04,735 adding 'lobster/tools/workspace_tool.py' 2026-01-06T11:07:04,738 adding 'lobster/tools/archive/publication_service.py' 2026-01-06T11:07:04,741 adding 'lobster/tools/archive/unified_content_service.py' 2026-01-06T11:07:04,743 adding 'lobster/tools/providers/__init__.py' 2026-01-06T11:07:04,745 adding 'lobster/tools/providers/abstract_provider.py' 2026-01-06T11:07:04,747 adding 'lobster/tools/providers/base_provider.py' 2026-01-06T11:07:04,749 adding 'lobster/tools/providers/biopython_entrez_wrapper.py' 2026-01-06T11:07:04,750 adding 'lobster/tools/providers/biorxiv_medrxiv_config.py' 2026-01-06T11:07:04,756 adding 'lobster/tools/providers/biorxiv_medrxiv_provider.py' 2026-01-06T11:07:04,762 adding 'lobster/tools/providers/geo_provider.py' 2026-01-06T11:07:04,764 adding 'lobster/tools/providers/geo_utils.py' 2026-01-06T11:07:04,766 adding 'lobster/tools/providers/massive_provider.py' 2026-01-06T11:07:04,769 adding 'lobster/tools/providers/ncbi_query_builder.py' 2026-01-06T11:07:04,771 adding 'lobster/tools/providers/organism_enum.py' 2026-01-06T11:07:04,773 adding 'lobster/tools/providers/pdb_provider.py' 2026-01-06T11:07:04,780 adding 'lobster/tools/providers/pmc_provider.py' 2026-01-06T11:07:04,782 adding 'lobster/tools/providers/pride_normalizer.py' 2026-01-06T11:07:04,785 adding 'lobster/tools/providers/pride_provider.py' 2026-01-06T11:07:04,787 adding 'lobster/tools/providers/provider_registry.py' 2026-01-06T11:07:04,790 adding 'lobster/tools/providers/publication_resolver.py' 2026-01-06T11:07:04,799 adding 'lobster/tools/providers/pubmed_provider.py' 2026-01-06T11:07:04,806 adding 'lobster/tools/providers/sra_provider.py' 2026-01-06T11:07:04,808 adding 'lobster/tools/providers/structure_provider.py' 2026-01-06T11:07:04,810 adding 'lobster/tools/providers/webpage_provider.py' 2026-01-06T11:07:04,812 adding 'lobster/ui/__init__.py' 2026-01-06T11:07:04,814 adding 'lobster/ui/console_manager.py' 2026-01-06T11:07:04,817 adding 'lobster/ui/live_dashboard.py' 2026-01-06T11:07:04,819 adding 'lobster/ui/progress_manager.py' 2026-01-06T11:07:04,821 adding 'lobster/ui/themes.py' 2026-01-06T11:07:04,823 adding 'lobster/ui/components/__init__.py' 2026-01-06T11:07:04,825 adding 'lobster/ui/components/file_tree.py' 2026-01-06T11:07:04,828 adding 'lobster/ui/components/multi_progress.py' 2026-01-06T11:07:04,829 adding 'lobster/ui/components/parallel_workers_progress.py' 2026-01-06T11:07:04,832 adding 'lobster/ui/components/status_display.py' 2026-01-06T11:07:04,833 adding 'lobster/ui/formatters/__init__.py' 2026-01-06T11:07:04,835 adding 'lobster/utils/__init__.py' 2026-01-06T11:07:04,841 adding 'lobster/utils/callbacks.py' 2026-01-06T11:07:04,842 adding 'lobster/utils/deviance.py' 2026-01-06T11:07:04,844 adding 'lobster/utils/error_handlers.py' 2026-01-06T11:07:04,847 adding 'lobster/utils/file_analyzer.py' 2026-01-06T11:07:04,849 adding 'lobster/utils/file_naming.py' 2026-01-06T11:07:04,851 adding 'lobster/utils/json_extractor.py' 2026-01-06T11:07:04,852 adding 'lobster/utils/logger.py' 2026-01-06T11:07:04,853 adding 'lobster/utils/progress_wrapper.py' 2026-01-06T11:07:04,855 adding 'lobster/utils/ssl_utils.py' 2026-01-06T11:07:04,856 adding 'lobster/utils/system.py' 2026-01-06T11:07:04,864 adding 'lobster_ai-0.4.0.7.dist-info/licenses/LICENSE' 2026-01-06T11:07:04,866 adding 'lobster_ai-0.4.0.7.dist-info/METADATA' 2026-01-06T11:07:04,867 adding 'lobster_ai-0.4.0.7.dist-info/WHEEL' 2026-01-06T11:07:04,868 adding 'lobster_ai-0.4.0.7.dist-info/entry_points.txt' 2026-01-06T11:07:04,869 adding 'lobster_ai-0.4.0.7.dist-info/top_level.txt' 2026-01-06T11:07:04,873 adding 'lobster_ai-0.4.0.7.dist-info/RECORD' 2026-01-06T11:07:04,890 removing build/bdist.linux-armv7l/wheel 2026-01-06T11:07:05,059 Building wheel for lobster-ai (pyproject.toml): finished with status 'done' 2026-01-06T11:07:05,089 Created wheel for lobster-ai: filename=lobster_ai-0.4.0.7-py3-none-any.whl size=1276895 sha256=cbee755d3f7ac5e1cd5b65bfe0309faa4acba90c1a6a1b32036010c45f0868d9 2026-01-06T11:07:05,090 Stored in directory: /tmp/pip-ephem-wheel-cache-ffmawshz/wheels/0a/eb/d9/a41fbfa352f05beb64b7acd0022e1ff851f7a13e7253a5cbc3 2026-01-06T11:07:05,115 Successfully built lobster-ai 2026-01-06T11:07:05,153 Removed build tracker: '/tmp/pip-build-tracker-gaagxmw1'