HISTORY.rst
LICENSE
Makefile
README.rst
dev-requirements.txt
mypy.ini
pyproject.toml
pytest.ini
setup.cfg
scripts/commit_version.py
scripts/new_version.py
scripts/print_version_for_release.py
src/galaxy/actions/__init__.py
src/galaxy/actions/library.py
src/galaxy/actions/py.typed
src/galaxy/agents/__init__.py
src/galaxy/agents/base.py
src/galaxy/agents/custom_tool.py
src/galaxy/agents/error_analysis.py
src/galaxy/agents/factory.py
src/galaxy/agents/gtn_training.py
src/galaxy/agents/history.py
src/galaxy/agents/history_tools.py
src/galaxy/agents/iwc.py
src/galaxy/agents/operations.py
src/galaxy/agents/orchestrator.py
src/galaxy/agents/page_assistant.py
src/galaxy/agents/py.typed
src/galaxy/agents/registry.py
src/galaxy/agents/router.py
src/galaxy/agents/static_backend.py
src/galaxy/agents/tools.py
src/galaxy/agents/workflow_report.py
src/galaxy/agents/gtn/__init__.py
src/galaxy/agents/gtn/__main__.py
src/galaxy/agents/gtn/build_database.py
src/galaxy/agents/gtn/search.py
src/galaxy/agents/prompts/custom_tool_container_critic.md
src/galaxy/agents/prompts/custom_tool_critic.md
src/galaxy/agents/prompts/custom_tool_structured.md
src/galaxy/agents/prompts/error_analysis.md
src/galaxy/agents/prompts/gtn_training.md
src/galaxy/agents/prompts/history_analyzer.md
src/galaxy/agents/prompts/orchestrator.md
src/galaxy/agents/prompts/page_assistant.md
src/galaxy/agents/prompts/router.md
src/galaxy/agents/prompts/tool_recommendation.md
src/galaxy/agents/prompts/workflow_report.md
src/galaxy/app/__init__.py
src/galaxy/app/py.typed
src/galaxy/app_unittest_utils/__init__.py
src/galaxy/app_unittest_utils/fetch_workbook.csv
src/galaxy/app_unittest_utils/fetch_workbook.tsv
src/galaxy/app_unittest_utils/fetch_workbook.xlsx
src/galaxy/app_unittest_utils/fetch_workbook_list_pairs_without_ids_example.xlsx
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src/galaxy/app_unittest_utils/fetch_workbook_paired.xlsx
src/galaxy/app_unittest_utils/fetch_workbook_paired_with_hashes.xlsx
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src/galaxy/authnz/auth0.py
src/galaxy/authnz/cilogon.py
src/galaxy/authnz/keycloak.py
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src/galaxy/dependencies/conditional-constraints.txt
src/galaxy/dependencies/conditional-requirements.txt
src/galaxy/dependencies/dev-requirements.txt
src/galaxy/dependencies/lint-requirements.txt
src/galaxy/dependencies/pinned-lint-requirements.txt
src/galaxy/dependencies/pinned-requirements.txt
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src/galaxy/jobs/runners/pulsar.py
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src/galaxy/managers/annotatable.py
src/galaxy/managers/api_keys.py
src/galaxy/managers/base.py
src/galaxy/managers/chat.py
src/galaxy/managers/citations.py
src/galaxy/managers/collections.py
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src/galaxy/managers/credentials.py
src/galaxy/managers/dataset_storage_operations.py
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src/galaxy/managers/datatypes.py
src/galaxy/managers/dbkeys.py
src/galaxy/managers/deletable.py
src/galaxy/managers/display_applications.py
src/galaxy/managers/executables.py
src/galaxy/managers/export_tracker.py
src/galaxy/managers/favorites.py
src/galaxy/managers/file_source_instances.py
src/galaxy/managers/folders.py
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src/galaxy/managers/genomes.py
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src/galaxy/managers/notification.py
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tests/app/tools/test_populate_state.py
tests/app/tools/test_resolution_cache_db.py
tests/app/tools/test_runtime.py
tests/app/tools/test_select_parameters.py
tests/app/tools/test_stock.py
tests/app/tools/test_tool_conf_repository.py
tests/app/tools/test_tool_dependency_description.py
tests/app/tools/test_tool_deserialization.py
tests/app/tools/test_tool_external_files.py
tests/app/tools/test_tool_serialization_roundtrip.py
tests/app/tools/test_tool_shed_repository_cache.py
tests/app/tools/test_toolbox.py
tests/app/tools/test_validation_parsing.py
tests/app/tools/test_wrappers.py
tests/app/tools/util.py
tests/app/visualizations/__init__.py
tests/app/visualizations/plugins/__init__.py
tests/app/visualizations/plugins/test_VisualizationPlugin.py
tests/app/visualizations/plugins/test_VisualizationsRegistry.py
tool-data/shared/ucsc/builds.txt.sample