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()
  • 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()
  • OpenCodeAgent
    • OpenCodeAgent.bin_env_key
    • OpenCodeAgent.build_exec_command()
    • OpenCodeAgent.default_binary
    • OpenCodeAgent.ensure_workspace_instruction_alias()
    • OpenCodeAgent.extract_assistant_text_chunk()
    • OpenCodeAgent.normalize_process_home()
    • OpenCodeAgent.prepare_final_reply_capture_command()
    • OpenCodeAgent.prepare_one_shot_exec_command()
    • OpenCodeAgent.prepare_runtime_env()
    • OpenCodeAgent.prepare_shared_turn_command()
    • OpenCodeAgent.provider
    • OpenCodeAgent.provider_id()
    • OpenCodeAgent.remove_workspace_instruction_alias_symlink()
    • OpenCodeAgent.render_stream_event()
    • OpenCodeAgent.resolve_binary()
    • OpenCodeAgent.resolve_binary_override()
    • OpenCodeAgent.sanitize_process_env()
    • OpenCodeAgent.service_env_overrides()
    • OpenCodeAgent.supports_auto_compile_metadata_generation()
    • OpenCodeAgent.supports_direct_terminal_stream()
    • OpenCodeAgent.uses_json_output_for_second_guess()
    • OpenCodeAgent.uses_json_stream()
    • OpenCodeAgent.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.gemini_agent module
      • GeminiAgent
    • fermilink.agents.opencode_agent module
      • OpenCodeAgent
    • 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_implement module
      • register_implement_parser()
    • fermilink.cli.parser_optimize module
      • register_optimize_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_drvloop_parser()
      • register_exec_loop_parsers()
      • register_exploop_parser()
    • fermilink.cli.parser_workflows module
      • register_workflow_parsers()
    • fermilink.cli.parser_workspace module
      • register_workspace_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.drvloop package
  • Submodules
    • fermilink.drvloop.artifacts module
      • detect_artifact_changes()
      • legacy_state_path_for()
      • load_state()
      • record_artifact_changes()
      • save_state()
      • snapshot_project_artifacts()
      • state_path_for()
    • fermilink.drvloop.instructions module
      • DrvloopInstructionFiles
      • materialize_drvloop_instructions()
    • fermilink.drvloop.main module
      • DrvloopConfig
      • build_drvloop_prompt()
      • cmd_drvloop()
      • main()
      • run_drvloop()
    • fermilink.drvloop.memory module
      • append_to_memory_section()
      • ensure_drvloop_memory()
      • memory_path_for()
    • fermilink.drvloop.prompts module
      • load_drvloop_guide()
• fermilink.exploop package
  • Submodules
    • fermilink.exploop.artifacts module
      • detect_artifact_changes()
      • legacy_state_path_for()
      • load_state()
      • record_artifact_changes()
      • save_state()
      • snapshot_project_artifacts()
      • state_path_for()
    • fermilink.exploop.instructions module
      • ExploopInstructionFiles
      • materialize_exploop_instructions()
    • fermilink.exploop.main module
      • ExploopConfig
      • build_exploop_prompt()
      • cmd_exploop()
      • main()
      • run_exploop()
    • fermilink.exploop.memory module
      • append_to_memory_section()
      • ensure_exploop_memory()
      • memory_path_for()
    • fermilink.exploop.pid module
      • is_pid_alive()
    • fermilink.exploop.prompts module
      • extract_pid_numbers()
      • extract_wait_seconds()
      • load_exploop_guide()
• fermilink.implement package
  • read_campaign_status()
  • run_goal_campaign()
  • Submodules
    • fermilink.implement.campaign module
      • read_campaign_status()
      • run_goal_campaign()
    • fermilink.implement.contract module
      • build_default_contract()
      • campaign_config()
      • controller_config()
      • editable_paths()
      • immutable_paths()
      • infer_workload_split()
      • load_contract()
      • normalize_command_list()
      • pre_commands()
      • scoring_config()
      • validate_contract()
      • validation_commands()
      • worker_config()
      • worker_visible_contract()
      • workload_split()
      • write_contract()
    • fermilink.implement.git module
      • checkout_implement_branch()
      • ensure_worker_worktree()
      • worker_branch_name()
      • worker_storage_root()
      • worker_worktree_path()
    • fermilink.implement.goal module
      • is_goal_markdown()
      • parse_goal()
      • render_worker_visible_goal()
    • fermilink.implement.main module
      • build_run_parser()
      • build_status_parser()
      • main()
    • fermilink.implement.prompts module
      • build_controller_agents_md()
      • build_controller_prompt()
      • build_worker_agents_md()
      • build_worker_prompt()
      • controller_review_decision()
      • controller_review_summary()
      • default_program_markdown()
      • extract_controller_review()
      • extract_controller_summary()
      • extract_decision()
      • extract_implementation_description()
    • fermilink.implement.source_analysis module
      • build_contract_generation_agents_md()
      • build_contract_generation_prompt()
      • build_source_analysis_agents_md()
      • build_source_analysis_prompt()
      • extract_analysis_summary()
      • extract_implementation_contract()
      • extract_review_notes()
      • extract_source_analysis()
      • extract_validation_runner()
    • fermilink.implement.state module
      • append_result()
      • archive_worker_memory()
      • autogen_root()
      • clear_run_lock()
      • contract_path()
      • ensure_autogen_root()
      • ensure_executable()
      • ensure_implement_root()
      • ensure_memory_file()
      • ensure_program_file()
      • ensure_results_file()
      • goal_analysis_path()
      • goal_copy_path()
      • implement_root()
      • load_json_file()
      • load_state()
      • memory_path()
      • pid_is_running()
      • plan_path()
      • program_path()
      • recent_results_text()
      • reset_worker_memory_file()
      • results_path()
      • run_lock_path()
      • runs_root()
      • safe_relative()
      • state_path()
      • utc_now_z()
      • validation_runner_path()
      • worker_memory_path()
      • write_json_file()
      • write_state()
    • fermilink.implement.validation module
      • acceptance_decision()
      • controller_review_final_ok()
      • expand_command()
      • final_integrity_ok()
      • run_pre_commands()
      • run_validation_suite()
      • validation_complete()
      • validation_score()
• fermilink.optimize package
  • Submodules
    • fermilink.optimize.benchmark module
    • fermilink.optimize.campaign module
      • read_campaign_status()
      • run_campaign()
      • run_goal_campaign()
      • run_quick_campaign()
    • fermilink.optimize.git module
      • branch_exists()
      • checkout_optimize_branch()
      • clean_worker_untracked()
      • cleanup_paths()
      • cleanup_stale_temporary_optimize_agents()
      • commit_paths()
      • current_branch()
      • ensure_clean_repo()
      • ensure_local_excludes()
      • ensure_worker_worktree()
      • head_sha()
      • inspect_worker_git_metadata()
      • list_changed_paths()
      • list_untracked_paths()
      • reset_to_commit()
      • reset_worker_to_commit()
      • restore_worker_git_metadata()
      • run_git()
      • temporary_optimize_agents()
      • with_worker_git_disabled()
      • worker_branch_name()
      • worker_worktree_path()
    • fermilink.optimize.goal module
      • is_goal_markdown()
      • parse_goal()
    • fermilink.optimize.goal_pipeline module
    • fermilink.optimize.main module
      • read_campaign_status()
      • run_campaign()
      • run_goal_campaign()
      • run_quick_campaign()
    • fermilink.optimize.prompts module
      • build_controller_agents_md()
      • build_controller_prompt()
      • build_optimize_agents_md()
      • build_optimize_prompt()
      • default_program_markdown()
      • extract_controller_summary()
      • extract_decision()
      • extract_experiment_description()
    • fermilink.optimize.source_analysis module
      • build_benchmark_generation_agents_md()
      • build_benchmark_generation_prompt()
      • build_source_analysis_agents_md()
      • build_source_analysis_prompt()
      • extract_analysis_summary()
      • extract_benchmark_yaml()
      • extract_review_notes()
      • extract_runner_script()
      • extract_source_analysis()
    • fermilink.optimize.state module
      • append_result()
      • archive_worker_memory()
      • autogen_root()
      • clear_run_lock()
      • default_program_path()
      • ensure_autogen_root()
      • ensure_executable()
      • ensure_memory_file()
      • ensure_optimize_root()
      • ensure_program_file()
      • ensure_results_file()
      • goal_analysis_path()
      • goal_benchmark_path()
      • goal_copy_path()
      • goal_inputs_all_root()
      • goal_inputs_manifest_path()
      • goal_inputs_worker_root()
      • goal_manifest_path()
      • goal_run_script_path()
      • goal_runner_path()
      • goal_setup_path()
      • goal_submit_launcher_path()
      • inputs_root()
      • load_json_file()
      • load_run_lock()
      • load_state()
      • memory_path()
      • optimize_root()
      • pid_is_running()
      • quick_benchmark_path()
      • quick_manifest_path()
      • quick_run_script_path()
      • quick_runner_path()
      • quick_setup_path()
      • quick_submit_launcher_path()
      • recent_results_text()
      • record_campaign_event()
      • reset_worker_memory_file()
      • results_path()
      • run_lock_path()
      • runs_root()
      • safe_relative()
      • state_path()
      • utc_now_z()
      • worker_benchmark_path()
      • worker_memory_path()
      • write_json_file()
      • write_run_lock()
      • write_state()
• 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_git_url()
      • install_from_local_path()
      • install_from_zip()
      • iter_package_entries()
      • list_packages()
      • load_registry()
      • load_workspace_manifest()
      • normalize_package_id()
      • normalize_package_workflow_type()
      • 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
• fermilink.workspace package
  • clean_package_workspace()
  • clean_workspace()
  • cmd_clean()
  • cmd_hpc()
  • cmd_init()
  • fermilink_clean_main()
  • fermilink_init_main()
  • initialize_package_workspace()
  • initialize_workspace()
  • Submodules
    • fermilink.workspace.clean module
      • clean_package_workspace()
      • clean_workspace()
      • cmd_clean()
      • fermilink_clean_main()
    • fermilink.workspace.common module
      • load_runner_app_module()
      • load_runner_scipkg_module()
      • resolve_cli_path()
      • resolve_exploop_agents_source()
      • resolve_software_agents_source()
    • fermilink.workspace.filesystem module
      • directories_match()
      • ensure_copied_directory()
      • ensure_symlink()
      • files_match()
      • path_exists()
      • remove_managed_copied_directory()
      • remove_managed_symlink()
      • remove_path()
      • symlink_matches()
    • fermilink.workspace.hpc module
      • cmd_hpc()
      • default_hpc_profile_path()
      • ensure_default_hpc_profile()
      • legacy_hpc_profile_path()
      • load_hpc_profile_payload()
      • normalize_hpc_profile_payload()
      • set_hpc_profile()
    • fermilink.workspace.init module
      • cmd_init()
      • fermilink_init_main()
      • initialize_package_workspace()
      • initialize_workspace()
    • fermilink.workspace.main module
      • clean_package_workspace()
      • clean_workspace()
      • cmd_clean()
      • cmd_hpc()
      • cmd_init()
      • fermilink_clean_main()
      • fermilink_init_main()
      • initialize_package_workspace()
      • initialize_workspace()
    • fermilink.workspace.payload module
      • ensure_agents_aliases()
      • ensure_agents_file()
      • ensure_valid_payload_root()
      • is_valid_payload_root()
      • iter_payload_entries()
      • managed_agents_symlink_sources()
      • remove_agents_aliases()
      • remove_managed_agents_file()
      • repo_root_fallback()
      • resolve_payload_agents_source()
      • resolve_payload_root()

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()