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FermiLink 0.2.1
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FermiLink 0.2.1
  • FermiLink
    • Introduction
    • Installation
    • Laptop Tutorial
    • HPC Tutorial
    • Usage Guide
      • Command Line Tools
      • Web UI
      • Chat Apps
      • Built-In Scientific Package Management
      • Configure Your Package
      • Reusable Research Pipelines and Memory
      • List of Built-in Scientific Packages
    • Advanced Configuration
    • Architecture
    • Contributing
    • API Reference
      • fermilink package
        • fermilink.agents package
          • fermilink.agents.base module
          • fermilink.agents.claude_agent module
          • fermilink.agents.codex_agent module
          • fermilink.agents.deepseek_agent module
          • fermilink.agents.gemini_agent module
          • fermilink.agents.registry module
        • fermilink.cli package
          • fermilink.cli.commands package
            • fermilink.cli.commands.agent module
            • fermilink.cli.commands.gateway module
            • fermilink.cli.commands.packages module
            • fermilink.cli.commands.services module
            • fermilink.cli.commands.sessions module
            • fermilink.cli.commands.workflows module
          • fermilink.cli.compile_helpers module
          • fermilink.cli.compile_prompts module
          • fermilink.cli.exec_runtime module
          • fermilink.cli.input_repo_helpers module
          • fermilink.cli.overlay_helpers module
          • fermilink.cli.parser_agent module
          • fermilink.cli.parser_builder module
          • fermilink.cli.parser_gateway module
          • fermilink.cli.parser_packages module
          • fermilink.cli.parser_services module
          • fermilink.cli.parser_sessions module
          • fermilink.cli.parser_workflows module
          • fermilink.cli.routing_helpers module
          • fermilink.cli.runtime_loaders module
          • fermilink.cli.shared_helpers module
          • fermilink.cli.workflow_prompts module
          • fermilink.cli.zero_arg module
        • fermilink.packages package
          • fermilink.packages.curated_channels module
          • fermilink.packages.package_core module
          • fermilink.packages.package_registry module
        • fermilink.runner package
          • fermilink.runner.admission module
          • fermilink.runner.app module
          • fermilink.runner.scientific_packages module
        • fermilink.web package
          • fermilink.web.activity_helpers module
          • fermilink.web.app module
          • fermilink.web.artifact_helpers module
          • fermilink.web.auth_helpers module
          • fermilink.web.chat_helpers module
          • fermilink.web.package_router_helpers module
          • fermilink.web.package_session_helpers module
          • fermilink.web.runner_helpers module
          • fermilink.web.sqlite_helpers module
          • fermilink.web.status_helpers module
          • fermilink.web.storage_helpers module
        • fermilink.agent_runtime module
        • fermilink.config module
        • fermilink.providers module
        • fermilink.router_rules module
        • fermilink.services module
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fermilink package¶

FermiLink package.

Subpackages¶

  • fermilink.agents package
    • AgentRegistry
      • AgentRegistry.__init__()
      • AgentRegistry.all()
      • AgentRegistry.get()
      • AgentRegistry.provider_bin_default_map()
      • AgentRegistry.provider_bin_env_map()
    • ClaudeAgent
      • ClaudeAgent.REASONING_MAP
      • ClaudeAgent.SANDBOX_PERMISSION_MODE
      • ClaudeAgent.bin_env_key
      • ClaudeAgent.build_exec_command()
      • ClaudeAgent.default_binary
      • ClaudeAgent.ensure_workspace_instruction_alias()
      • ClaudeAgent.extract_assistant_text_chunk()
      • ClaudeAgent.normalize_process_home()
      • ClaudeAgent.prepare_final_reply_capture_command()
      • ClaudeAgent.prepare_one_shot_exec_command()
      • ClaudeAgent.prepare_runtime_env()
      • ClaudeAgent.prepare_shared_turn_command()
      • ClaudeAgent.provider
      • ClaudeAgent.provider_id()
      • ClaudeAgent.remove_workspace_instruction_alias_symlink()
      • ClaudeAgent.render_stream_event()
      • ClaudeAgent.resolve_binary()
      • ClaudeAgent.resolve_binary_override()
      • ClaudeAgent.sanitize_process_env()
      • ClaudeAgent.service_env_overrides()
      • ClaudeAgent.supports_auto_compile_metadata_generation()
      • ClaudeAgent.supports_direct_terminal_stream()
      • ClaudeAgent.uses_json_output_for_second_guess()
      • ClaudeAgent.uses_json_stream()
      • ClaudeAgent.workspace_instruction_alias_name()
    • CodexAgent
      • CodexAgent.bin_env_key
      • CodexAgent.build_exec_command()
      • CodexAgent.default_binary
      • CodexAgent.ensure_workspace_instruction_alias()
      • CodexAgent.extract_assistant_text_chunk()
      • CodexAgent.normalize_process_home()
      • CodexAgent.prepare_final_reply_capture_command()
      • CodexAgent.prepare_one_shot_exec_command()
      • CodexAgent.prepare_runtime_env()
      • CodexAgent.prepare_shared_turn_command()
      • CodexAgent.provider
      • CodexAgent.provider_id()
      • CodexAgent.remove_workspace_instruction_alias_symlink()
      • CodexAgent.render_stream_event()
      • CodexAgent.resolve_binary()
      • CodexAgent.resolve_binary_override()
      • CodexAgent.sanitize_process_env()
      • CodexAgent.service_env_overrides()
      • CodexAgent.supports_auto_compile_metadata_generation()
      • CodexAgent.supports_direct_terminal_stream()
      • CodexAgent.uses_json_output_for_second_guess()
      • CodexAgent.uses_json_stream()
      • CodexAgent.workspace_instruction_alias_name()
    • DeepseekAgent
      • DeepseekAgent.bin_env_key
      • DeepseekAgent.build_exec_command()
      • DeepseekAgent.default_binary
      • DeepseekAgent.ensure_workspace_instruction_alias()
      • DeepseekAgent.extract_assistant_text_chunk()
      • DeepseekAgent.normalize_process_home()
      • DeepseekAgent.prepare_final_reply_capture_command()
      • DeepseekAgent.prepare_one_shot_exec_command()
      • DeepseekAgent.prepare_runtime_env()
      • DeepseekAgent.prepare_shared_turn_command()
      • DeepseekAgent.provider
      • DeepseekAgent.provider_id()
      • DeepseekAgent.remove_workspace_instruction_alias_symlink()
      • DeepseekAgent.render_stream_event()
      • DeepseekAgent.resolve_binary()
      • DeepseekAgent.resolve_binary_override()
      • DeepseekAgent.sanitize_process_env()
      • DeepseekAgent.service_env_overrides()
      • DeepseekAgent.supports_auto_compile_metadata_generation()
      • DeepseekAgent.supports_direct_terminal_stream()
      • DeepseekAgent.uses_json_output_for_second_guess()
      • DeepseekAgent.uses_json_stream()
      • DeepseekAgent.workspace_instruction_alias_name()
    • GeminiAgent
      • GeminiAgent.bin_env_key
      • GeminiAgent.build_exec_command()
      • GeminiAgent.default_binary
      • GeminiAgent.ensure_workspace_instruction_alias()
      • GeminiAgent.extract_assistant_text_chunk()
      • GeminiAgent.normalize_process_home()
      • GeminiAgent.prepare_final_reply_capture_command()
      • GeminiAgent.prepare_one_shot_exec_command()
      • GeminiAgent.prepare_runtime_env()
      • GeminiAgent.prepare_shared_turn_command()
      • GeminiAgent.provider
      • GeminiAgent.provider_id()
      • GeminiAgent.remove_workspace_instruction_alias_symlink()
      • GeminiAgent.render_stream_event()
      • GeminiAgent.resolve_binary()
      • GeminiAgent.resolve_binary_override()
      • GeminiAgent.sanitize_process_env()
      • GeminiAgent.service_env_overrides()
      • GeminiAgent.supports_auto_compile_metadata_generation()
      • GeminiAgent.supports_direct_terminal_stream()
      • GeminiAgent.uses_json_output_for_second_guess()
      • GeminiAgent.uses_json_stream()
      • GeminiAgent.workspace_instruction_alias_name()
    • ProviderAgent
      • ProviderAgent.bin_env_key
      • ProviderAgent.build_exec_command()
      • ProviderAgent.default_binary
      • ProviderAgent.ensure_workspace_instruction_alias()
      • ProviderAgent.extract_assistant_text_chunk()
      • ProviderAgent.normalize_process_home()
      • ProviderAgent.prepare_final_reply_capture_command()
      • ProviderAgent.prepare_one_shot_exec_command()
      • ProviderAgent.prepare_runtime_env()
      • ProviderAgent.prepare_shared_turn_command()
      • ProviderAgent.provider
      • ProviderAgent.provider_id()
      • ProviderAgent.remove_workspace_instruction_alias_symlink()
      • ProviderAgent.render_stream_event()
      • ProviderAgent.resolve_binary()
      • ProviderAgent.resolve_binary_override()
      • ProviderAgent.sanitize_process_env()
      • ProviderAgent.service_env_overrides()
      • ProviderAgent.supports_auto_compile_metadata_generation()
      • ProviderAgent.supports_direct_terminal_stream()
      • ProviderAgent.uses_json_output_for_second_guess()
      • ProviderAgent.uses_json_stream()
      • ProviderAgent.workspace_instruction_alias_name()
    • get_default_agent_registry()
    • get_provider_agent()
    • Submodules
      • fermilink.agents.base module
        • ProviderAgent
        • insert_option_before_prompt()
      • fermilink.agents.claude_agent module
        • ClaudeAgent
      • fermilink.agents.codex_agent module
        • CodexAgent
      • fermilink.agents.deepseek_agent module
        • DeepseekAgent
      • fermilink.agents.gemini_agent module
        • GeminiAgent
      • fermilink.agents.registry module
        • AgentRegistry
        • get_default_agent_registry()
        • get_provider_agent()
  • fermilink.cli package
    • main()
    • Subpackages
      • fermilink.cli.commands package
        • Submodules
    • Submodules
      • fermilink.cli.compile_helpers module
      • fermilink.cli.compile_prompts module
      • fermilink.cli.exec_runtime module
      • fermilink.cli.input_repo_helpers module
      • fermilink.cli.overlay_helpers module
      • fermilink.cli.parser_agent module
        • register_agent_parser()
      • fermilink.cli.parser_builder module
      • fermilink.cli.parser_gateway module
        • register_gateway_parser()
      • fermilink.cli.parser_packages module
        • register_package_install_compile_parsers()
        • register_package_management_parsers()
      • fermilink.cli.parser_services module
        • register_service_parsers()
      • fermilink.cli.parser_sessions module
        • register_chat_parser()
        • register_exec_loop_parsers()
      • fermilink.cli.parser_workflows module
        • register_workflow_parsers()
      • fermilink.cli.routing_helpers module
      • fermilink.cli.runtime_loaders module
      • fermilink.cli.shared_helpers module
      • fermilink.cli.workflow_prompts module
      • fermilink.cli.zero_arg module
  • fermilink.packages package
    • atomic_write_json()
    • build_default_registry()
    • extract_manifest_dependency_ids()
    • extract_manifest_entry_names()
    • is_exportable_entry_name()
    • link_or_copy_entry()
    • load_registry_file()
    • normalize_package_id()
    • normalize_registry_payload()
    • overlay_package_into_repo_core()
    • remove_existing_entry()
    • remove_managed_dependency_links()
    • remove_managed_entries()
    • save_registry_file()
    • Submodules
      • fermilink.packages.curated_channels module
        • ChannelPackage
        • ChannelPackageVersion
        • list_curated_packages()
        • normalize_channel_id()
        • resolve_curated_package()
        • select_package_version()
      • fermilink.packages.package_core module
        • atomic_write_json()
        • build_default_registry()
        • extract_manifest_dependency_ids()
        • extract_manifest_entry_names()
        • is_exportable_entry_name()
        • link_or_copy_entry()
        • load_registry_file()
        • normalize_package_id()
        • normalize_registry_payload()
        • overlay_package_into_repo_core()
        • remove_existing_entry()
        • remove_managed_dependency_links()
        • remove_managed_entries()
        • save_registry_file()
      • fermilink.packages.package_registry module
        • PackageError
        • PackageNotFoundError
        • PackageValidationError
        • activate_package()
        • delete_package()
        • install_from_local_path()
        • install_from_zip()
        • iter_package_entries()
        • list_packages()
        • load_registry()
        • load_workspace_manifest()
        • normalize_package_id()
        • overlay_package_into_repo()
        • packages_root()
        • register_package()
        • registry_path()
        • resolve_session_package()
        • save_registry()
        • save_workspace_manifest()
        • set_package_dependency_ids()
        • set_package_overlay_entries()
        • workspace_manifest_path()
  • fermilink.runner package
    • Submodules
      • fermilink.runner.admission module
        • QueueFullError
        • RunAdmissionController
      • fermilink.runner.app module
        • RunRequest
        • find_project_root()
        • ops_admission()
        • ops_concurrency()
        • ops_concurrency_prometheus()
        • run()
        • sse()
        • verify_provider_bin()
      • fermilink.runner.scientific_packages module
        • PackageError
        • PackageNotFoundError
        • PackageValidationError
        • activate_package()
        • bootstrap_legacy_maxwelllink_package()
        • delete_package()
        • find_project_root()
        • iter_package_entries()
        • list_packages()
        • load_registry()
        • load_workspace_manifest()
        • normalize_package_id()
        • overlay_package_into_repo()
        • packages_root()
        • register_package()
        • registry_path()
        • resolve_scipkg_root()
        • resolve_session_package()
        • save_workspace_manifest()
        • set_package_dependency_ids()
        • set_package_overlay_entries()
        • workspace_manifest_path()
  • fermilink.web package
    • Submodules
      • fermilink.web.activity_helpers module
      • fermilink.web.app module
      • fermilink.web.artifact_helpers module
      • fermilink.web.auth_helpers module
      • fermilink.web.chat_helpers module
      • fermilink.web.package_router_helpers module
      • fermilink.web.package_session_helpers module
      • fermilink.web.runner_helpers module
      • fermilink.web.sqlite_helpers module
      • fermilink.web.status_helpers module
      • fermilink.web.storage_helpers module
        • LocalPublicStorageClient

Submodules¶

  • fermilink.agent_runtime module
    • AgentRuntimePolicy
      • AgentRuntimePolicy.__init__()
      • AgentRuntimePolicy.as_dict()
      • AgentRuntimePolicy.as_env()
      • AgentRuntimePolicy.model
      • AgentRuntimePolicy.provider
      • AgentRuntimePolicy.reasoning_effort
      • AgentRuntimePolicy.sandbox_mode
      • AgentRuntimePolicy.sandbox_policy
    • load_agent_runtime_policy()
    • normalize_model()
    • normalize_provider()
    • normalize_reasoning_effort()
    • normalize_sandbox_mode()
    • normalize_sandbox_policy()
    • resolve_agent_runtime_path()
    • resolve_agent_runtime_policy()
    • save_agent_runtime_policy()
  • fermilink.config module
    • resolve_fermilink_home()
    • resolve_runtime_root()
    • resolve_scipkg_root()
    • resolve_workspaces_root()
  • fermilink.providers module
    • build_exec_command()
    • collect_provider_service_env_overrides()
    • provider_bin_env_key()
    • provider_supports_auto_compile_metadata_generation()
    • resolve_provider_binary()
    • resolve_provider_binary_override()
  • fermilink.router_rules module
    • build_synced_rules()
    • dedupe()
    • infer_rule()
    • load_family_hints()
    • normalize_terms()
    • package_id_terms()
    • sync_router_rules()
  • fermilink.services module
    • ServiceSpec
      • ServiceSpec.__init__()
      • ServiceSpec.command
      • ServiceSpec.env
      • ServiceSpec.name
    • default_service_specs()
    • normalize_components()
    • service_status()
    • start_service()
    • stop_service()
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