Functions — github.com/ChicagoHAI/NeuriCo

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Functions1,808 in github.com/ChicagoHAI/NeuriCo

⨍ Functions 1,808◇ Types & classes 448↳ Endpoints 5

↓ 3 callersMethodbuild

Build the operation with a specific factory.

services/paper-finder/agents/mabool/api/mabool/agents/metadata_only/ops.py:41

↓ 3 callersFunctioncheck_if_paper_inserted_before

( last_allowed_pub_date: date | None, year: int | None, publication_date: date | None )

services/paper-finder/libs/dcollection/ai2i/dcollection/fetchers/s2.py:72

↓ 3 callersMethodcheckpoint_exists

Return whether a commit object exists in this workspace repository.

src/core/autoresearch.py:378

↓ 3 callersMethodclone_with

(self, providers: Providers, pre_populated_cache: CachedValues | None = None)

services/paper-finder/libs/di/ai2i/di/managed_env.py:50

↓ 3 callersMethodcomplete_attempt

Fill in the post-comment-mode artifacts for an existing attempt.

src/core/autoresearch.py:539

↓ 3 callersFunctioncounted_noun

(base: str, count: int)

services/paper-finder/agents/mabool/api/mabool/agents/common/step_reporting_utils.py:24

↓ 3 callersMethodcreate_fresh_scopes_context

(self, *, patched_instances: dict[str, Any])

services/paper-finder/libs/di/ai2i/di/app_context.py:50

↓ 3 callersMethoddestroy

(self, round_id: RoundId)

services/paper-finder/libs/di/ai2i/di/rounds_storage.py:50

↓ 3 callersMethoddigest_section

Compact text the manager sees each turn as part of its system prompt. Kept bounded so it never crowds out the conversation. This is the

src/interactive/research_state.py:562

↓ 3 callersFunctiondsi_slurm_remote_workspace

Runtime lifecycle shell for dsi-slurm stages. No-op unless --compute-backend is exactly dsi-slurm.

src/core/dsi_slurm_remote.py:136

↓ 3 callersMethodemit_raw

Push a pre-formatted event (used by the agent-log tailer).

src/interactive/channel.py:166

↓ 3 callersFunctionexternal_dynamic_field

( *args: Any, fuse: Fuser[DocumentFieldName] = TakeFirst(), **kwargs: Any, )

services/paper-finder/libs/dcollection/ai2i/dcollection/interface/collection.py:88

↓ 3 callersMethodformat

(self, record: logging.LogRecord)

services/paper-finder/agents/mabool/api/mabool/utils/logging.py:29

↓ 3 callersMethodfrom_dense_retrieval

( queries: list[str], search_iteration: int, dataset: DenseDataset, top_k: int

services/paper-finder/agents/mabool/api/mabool/utils/dc.py:114

↓ 3 callersMethodfrom_s2_by_author

( authors_profiles: list[list[Any]], limit: int, dcf: DocumentCollectionFactory = DI.r

services/paper-finder/agents/mabool/api/mabool/utils/dc.py:52

↓ 3 callersMethodfrom_s2_by_title

( query: str, time_range: ExtractedYearlyTimeRange | None = None, venues: list[str] |

services/paper-finder/agents/mabool/api/mabool/utils/dc.py:64

↓ 3 callersFunctiongenerate_instructions

Generate comprehensive session instructions for the research agent. This is a convenience wrapper that uses PromptGenerator internally.

templates/research_agent_instructions.py:37

↓ 3 callersMethodget_actual_vespa_version

(self)

services/paper-finder/libs/dcollection/ai2i/dcollection/external_api/dense/vespa.py:151

↓ 3 callersFunctionget_runtime_compute_backend

Read the CLI-selected backend. Missing means local.

src/core/compute_backend.py:37

↓ 3 callersMethodgpt4o

(**params: Unpack[LLMModelParams])

services/paper-finder/libs/chain/ai2i/chain/models.py:96

↓ 3 callersFunctiongreet

(name: str)

services/paper-finder/agents/mabool/api/mabool/services/tests/test_prioritized_task.py:150

↓ 3 callersMethodlookup_key

(self, entity_id: EntityId, field_name: DFN)

services/paper-finder/libs/dcollection/ai2i/dcollection/caching/cache.py:294

↓ 3 callersMethodmark_completed

Mark entire pipeline as completed.

src/core/pipeline_orchestrator.py:96

↓ 3 callersMethodnext_attempt_dir

(self, parent_sha: str)

src/core/autoresearch.py:495

↓ 3 callersMethodnormalize

(self)

services/paper-finder/agents/mabool/api/mabool/data_model/specifications.py:187

↓ 3 callersFunctionnormalize_domain

Normalize a domain, falling back to default if invalid. Args: domain: Domain to normalize Returns: Valid domain name (o

src/core/config_loader.py:297

↓ 3 callersMethodopen_scope

(self, values: CachedValues | None = None)

services/paper-finder/libs/di/ai2i/di/scopes.py:92

↓ 3 callersFunctionplan

(specifications: specs.Specifications)

services/paper-finder/agents/mabool/api/mabool/agents/metadata_only/plan.py:540

↓ 3 callersFunctionpluralize

(base: str, count: int)

services/paper-finder/agents/mabool/api/mabool/agents/common/step_reporting_utils.py:20

↓ 3 callersMethodpriority_context

(self, priority: int = DEFAULT_PRIORITY)

services/paper-finder/agents/mabool/api/mabool/services/prioritized_task.py:79

↓ 3 callersMethodproduct

(self, p: ChainComputation[IN, OUT2])

services/paper-finder/libs/chain/ai2i/chain/computation.py:175

↓ 3 callersMethodproject

(self, map_fn: DocumentProjector[V])

services/paper-finder/libs/dcollection/ai2i/dcollection/interface/collection.py:286

↓ 3 callersFunctionproject_root

()

services/paper-finder/agents/mabool/api/mabool/utils/paths.py:6

↓ 3 callersFunctionread_autoresearch_state

Read AutoResearch continuation state, returning an empty dict when absent/invalid.

src/core/autoresearch.py:95

↓ 3 callersMethodread_from_dict

(self, d: dict[str, Any])

services/paper-finder/libs/config/ai2i/config/config_models.py:78

↓ 3 callersFunctionremote_workspace_info_path

(work_dir: Path)

src/core/dsi_slurm_remote.py:25

↓ 3 callersFunctionresolve_autoresearch_history_root

Resolve the AutoResearch history root from CLI, state, or default.

src/core/autoresearch.py:148

↓ 3 callersMethodrestore_checkpoint

Restore tracked workspace files to a checkpoint. By default this avoids `git clean` so ignored datasets, venvs, and other lo

src/core/autoresearch.py:349

↓ 3 callersMethodrun

Execute AutoResearch iterations from the current scored workspace state. The initial checkpoint is created from the already-scored p

src/core/autoresearch.py:1531

↓ 3 callersMethodrun_paper_finder_on_analyzed_query

( self, inputs: PaperFinderInput, analyzed_input: AnalyzedQuery, anchor_docs: DocumentCollection )

services/paper-finder/agents/mabool/api/mabool/agents/paper_finder/paper_finder_agent.py:247

↓ 3 callersFunctionscore_by_rank

(collection: DocumentCollection, max_score: int = 3)

services/paper-finder/agents/mabool/api/mabool/agents/specific_paper_by_name/specific_paper_by_name_agent.py:277

↓ 3 callersFunctionscoring_func

( extracted_name: str, found_in_search_with_content: int, title: str, abstract

services/paper-finder/agents/mabool/api/mabool/agents/specific_paper_by_name/specific_paper_by_name_agent.py:146

↓ 3 callersMethodshould_allow_unknown_domains

Check if unknown domains should be allowed (with fallback). Returns: True if unknown domains are allowed

src/core/config_loader.py:107

↓ 3 callersMethodstatus

(self, label: str = "", *, thinking: bool = False, waiting: bool = False, phase: str = "")

src/interactive/channel.py:179

↓ 3 callersFunctionstep

(name: str, cmd: List[str])

templates/skills/modal-training/scripts/_doctor_checks.py:219

↓ 3 callersMethodsubmit_idea

Submit a new research idea. Args: idea_spec: Idea specification dictionary validate: Whether to validate aga

src/core/idea_manager.py:64

↓ 3 callersMethodto_flat_criteria

(self, include_nice_to_have: bool = True)

services/paper-finder/libs/dcollection/ai2i/dcollection/interface/document.py:369

↓ 3 callersFunctionto_reward

(doc: Document, field: str)

services/paper-finder/libs/dcollection/ai2i/dcollection/loaders/adaptive.py:140

↓ 3 callersMethodvalidate_idea

Validate idea specification. Args: idea_spec: Idea specification dictionary Returns: Dictionary wit

src/core/idea_manager.py:107

↓ 3 callersFunctionverbalize_list

(items: list[str], connector: Literal["and", "or"])

services/paper-finder/agents/mabool/api/mabool/agents/common/step_reporting_utils.py:4

↓ 3 callersFunctionwith_priority

( func: Callable[P, Awaitable[T]], semaphore: PrioritySemaphore, priority: int = DEFAULT_PRIORITY )

services/paper-finder/agents/mabool/api/mabool/services/prioritized_task.py:100

↓ 3 callersFunctionwithout_runtime_compute_backend

Return a copy with transient backend markers removed before persistence.

src/core/compute_backend.py:47

↓ 3 callersFunctionworkspace_root

Walk upward from `start` (or cwd) looking for a directory containing `.neurico/`. Falls back to the starting directory if no marker is found.

templates/skills/modal-training/scripts/lifecycle.py:65

↓ 3 callersFunctionwrite_autoresearch_state

Persist enough state for a later --continue-autoresearch run.

src/core/autoresearch.py:175

↓ 2 callersMethod__call__

(self)

services/paper-finder/agents/mabool/api/mabool/agents/metadata_only/ops.py:65

↓ 2 callersMethod__init__

( self, scope: ScopeOrCustom, providers: Providers, patched_instances: dict[str, Any] | None = None

services/paper-finder/libs/di/ai2i/di/scopes.py:75

↓ 2 callersMethod_add_to_loaded_fields

(self, key: str)

services/paper-finder/libs/dcollection/ai2i/dcollection/document.py:136

↓ 2 callersMethod_clear_stale_results_json

(self)

src/core/autoresearch.py:1807

↓ 2 callersFunction_count_files

(*dirs: Path)

src/interactive/web_server.py:149

↓ 2 callersFunction_count_relevance_by_level

(collection: DocumentCollection)

services/paper-finder/agents/mabool/api/mabool/agents/common/explain.py:125

↓ 2 callersFunction_create_and_wait_for_tasks

( session_id: str, operative_task: asyncio.Task[OperativeResponse[OUTPUT]], timeout: float = Confi

services/paper-finder/agents/mabool/api/mabool/infra/operatives/interaction.py:123

↓ 2 callersFunction_deep_lowercase_keys

(d: dict[str, Any])

services/paper-finder/libs/config/ai2i/config/loading.py:100

↓ 2 callersMethod_ensure_results_json

Ensure a public scoring/results.json exists for node traceability. If the scorer fails before producing results.json, write a small

src/core/autoresearch.py:1760

↓ 2 callersFunction_extract_round_context

(request: Request, request_and_body: RequestAndBody)

services/paper-finder/agents/mabool/api/mabool/utils/context_deps.py:31

↓ 2 callersMethod_extract_user_instructions

Extract user-provided instructions from the prompt. Looks for content in the "User-Provided Instructions and Context" section

src/templates/prompt_generator.py:746

↓ 2 callersMethod_fetch_from_operatives

( self, operatives: list[SearchOperative], docs: DocumentCollection )

services/paper-finder/agents/mabool/api/mabool/agents/complex_search/broad_search.py:184

↓ 2 callersFunction_fetch_paper_data

( corpus_ids: Sequence[int], fields: Sequence[DocumentFieldName], s2_client: AsyncSemanticScholar,

services/paper-finder/libs/dcollection/ai2i/dcollection/loaders/s2_rest.py:126

↓ 2 callersMethod_follow_key

(self, d: dict[str, Any], key: str)

services/paper-finder/libs/config/ai2i/config/config_models.py:94

↓ 2 callersFunction_function_signature

(node: ast.AST)

src/core/workspace_manifest.py:246

↓ 2 callersFunction_fuzzy_find_snippet_text

(text: str, snippet_to_find: str)

services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevant_snippets.py:110

↓ 2 callersMethod_generate_compute_backend_section

Generate operational compute-backend constraints for execution agents. Missing --compute-backend means local and intentionally emits

src/templates/prompt_generator.py:554

↓ 2 callersFunction_get_current_git_sha

()

services/paper-finder/agents/mabool/api/mabool/utils/file_based_cache.py:16

↓ 2 callersMethod_get_dynamic_field

(self, field_name: DocumentFieldName)

services/paper-finder/libs/dcollection/ai2i/dcollection/collection.py:166

↓ 2 callersFunction_get_qualified_name

(f: AsyncFunc[..., A] | AsyncContextFunc[..., A])

services/paper-finder/libs/di/ai2i/di/providers.py:215

↓ 2 callersMethod_handle_exit

Save session and exit.

src/interactive/manager.py:469

↓ 2 callersFunction_is_hidden_context_path

(rel_path: str)

src/agents/autoresearch_proposer.py:382

↓ 2 callersMethod_is_set_type

Check if a node represents a set type.

services/paper-finder/dev/python/flake8_plugins/stable_sort_checker.py:32

↓ 2 callersMethod_matching_workspace_paths

(self, patterns: Iterable[str])

src/core/autoresearch.py:466

↓ 2 callersMethod_merge_doc_source_responses

( self, docs: DocumentCollection, doc_source_responses: Sequence[OperativeResponse] )

services/paper-finder/agents/mabool/api/mabool/agents/complex_search/broad_search.py:229

↓ 2 callersMethod_move_dsi_slurm_artifacts_to_attempt

(self, attempt_dir: Path)

src/core/autoresearch.py:1812

↓ 2 callersMethod_normalize_options

Coerce options to the v3 shape ``[{text, status}]``. Accepts a list of bare strings (legacy / convenience) or a list of dicts. Each option's

src/interactive/research_state.py:202

↓ 2 callersFunction_order_lean

(paths: List[Path])

templates/skills/axiom-lean-prover/scripts/axle_check.py:74

↓ 2 callersFunction_read_json_or_text

(path: Path)

src/agents/autoresearch_proposer.py:333

↓ 2 callersMethod_record_failed_before_checkpoint

( self, attempt_dir: Path, parent_sha: str, results_path: Path, decisi

src/core/autoresearch.py:1818

↓ 2 callersMethod_register_dependency

(self, definition: DependencyDefinition[A])

services/paper-finder/libs/di/ai2i/di/providers.py:163

↓ 2 callersMethod_run_paper_writer_stage

( self, idea: Dict[str, Any], work_dir: Path, provider: str, paper_sty

src/core/runner.py:898

↓ 2 callersMethod_run_scorer

Run the scorer stage (scoring mode only). Executes scoring/eval.py and captures the structured results into scoring/results.json.

src/core/pipeline_orchestrator.py:748

↓ 2 callersFunction_safe_header_text

(text: str)

src/core/workspace_manifest.py:475

↓ 2 callersMethod_setup_personal_account

Configure GitHub manager to use the authenticated user's personal account.

src/core/github_manager.py:108

↓ 2 callersFunction_sub_task

()

services/paper-finder/libs/di/ai2i/di/tests/test_app_context.py:158

↓ 2 callersMethod_update_computed_fields

(self, fields: Sequence[DocumentFieldName | BaseComputedField])

services/paper-finder/libs/dcollection/ai2i/dcollection/collection.py:181

↓ 2 callersMethod_wrap_value

(self, value: Any)

services/paper-finder/libs/config/ai2i/config/config_models.py:14

↓ 2 callersMethodabatch

( self, inputs: list[IN], config: RunnableConfig | list[RunnableConfig] | None = None,

services/paper-finder/libs/chain/ai2i/chain/endpoints.py:257

↓ 2 callersFunctionarchive_dsi_slurm_artifacts

Move transient DSI artifacts into the normal logs archive.

src/core/dsi_slurm_artifacts.py:53

↓ 2 callersMethodas_dict

(self)

src/core/workspace_manifest.py:852

↓ 2 callersFunctionautoresearch_state_current_best_sha

Return the current best node.

src/core/autoresearch.py:113

↓ 2 callersFunctionautoresearch_state_lineage_source_sha

Return the first scored node for this lineage.

src/core/autoresearch.py:107

↓ 2 callersFunctionbootstrap_baseline_state_path

Return the per-workspace bootstrap baseline construction state path.

src/core/autoresearch.py:78

↓ 2 callersMethodbuild

Build a cache keys lookup for the given entities and fields.

services/paper-finder/libs/dcollection/ai2i/dcollection/caching/cache.py:260

↓ 2 callersFunctionbuild_manifest

Build a deterministic, value-redacted manifest of a workspace. The manifest is the only structural information the bootstrap rule_maker

src/core/workspace_manifest.py:659

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