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github.com/ChicagoHAI/NeuriCo
/ functions
Functions
1,808 in github.com/ChicagoHAI/NeuriCo
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Functions
1,808
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Types & classes
448
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Endpoints
5
↓ 1 callers
Method
__init__
(self, decorated: Runnable[IN, OUT], retry_settings: TenacityRetrySettings)
services/paper-finder/libs/chain/ai2i/chain/endpoints.py:242
↓ 1 callers
Method
__init__
(self, message: Optional[str] = None)
services/paper-finder/agents/mabool/api/mabool/data_model/agent.py:219
↓ 1 callers
Function
_add_missing_fields_and_sort
( initial_docs: DocumentCollection, plan_context: PlanContext )
services/paper-finder/agents/mabool/api/mabool/agents/paper_finder/paper_finder_agent.py:92
↓ 1 callers
Method
_agenerate_message
( self, messages: Sequence[BaseMessage], stop: list[str] | None = None, **kwargs: Any )
services/paper-finder/libs/chain/ai2i/chain/gemini/async_genai.py:53
↓ 1 callers
Method
_agent_step
Execute one step of the agent loop.
src/interactive/manager.py:333
↓ 1 callers
Function
_align_ref_mentions
( snippet: Snippet, sentences: list[Snippet], sentence_offsets: list[SentenceOffsets] )
services/paper-finder/agents/mabool/api/mabool/agents/snowball/snippet_snowball.py:185
↓ 1 callers
Method
_apply_all_values
( self, entities: Sequence[DynamicallyLoadedEntity[DFN]], fields: set[DFN], ca
services/paper-finder/libs/dcollection/ai2i/dcollection/caching/cache.py:114
↓ 1 callers
Method
_apply_relevance_judgement
(self, docs: DocumentCollection)
services/paper-finder/agents/mabool/api/mabool/agents/complex_search/broad_search.py:240
↓ 1 callers
Function
_async_context_adapter
( context_factory: AsyncContextFunc[..., A], provider_name: str )
services/paper-finder/libs/di/ai2i/di/providers.py:189
↓ 1 callers
Function
_async_factory_adapter
( factory: AsyncFactory[A], provider_name: str )
services/paper-finder/libs/di/ai2i/di/providers.py:174
↓ 1 callers
Function
_auth_source
Identify which auth path the CLI is using. The Modal CLI honors MODAL_TOKEN_ID / MODAL_TOKEN_SECRET first, then ~/.modal.toml. In the Do
templates/skills/modal-training/scripts/_doctor_checks.py:70
↓ 1 callers
Function
_batched_from_s2
(entities: Sequence[Document], fields: Sequence[DocumentFieldName])
services/paper-finder/libs/dcollection/ai2i/dcollection/loaders/s2_rest.py:55
↓ 1 callers
Method
_bootstrap_sealed_dir_for
Sibling sealed dir for bootstrap mode.
src/core/pipeline_orchestrator.py:1015
↓ 1 callers
Function
_brand_file
(project_root: Path, key: str)
src/interactive/web_server.py:832
↓ 1 callers
Method
_build_all
(self)
services/paper-finder/libs/di/ai2i/di/managed_env.py:68
↓ 1 callers
Function
_build_merged_response_potentially_relevant
(prev_summary: str, relevant_docs: Sequence[Document])
services/paper-finder/agents/mabool/api/mabool/agents/common/explain.py:243
↓ 1 callers
Function
_build_merged_response_with_perfect_matches
( prev_summary: str, perfect_count: int, high_count: int, other_count: int )
services/paper-finder/agents/mabool/api/mabool/agents/common/explain.py:250
↓ 1 callers
Function
_build_merged_response_without_perfect_matches
(prev_summary: str, high_count: int, other_count: int)
services/paper-finder/agents/mabool/api/mabool/agents/common/explain.py:274
↓ 1 callers
Function
_build_relevance_criteria_judgements
( doc: Document, judgement_data: list[dict[str, Any]] )
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevance.py:389
↓ 1 callers
Function
_build_relevance_judgement
Build the final RelevanceJudgement object.
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevance.py:362
↓ 1 callers
Function
_build_response_with_perfect_matches
(perfect_count: int, high_count: int, other_count: int)
services/paper-finder/agents/mabool/api/mabool/agents/common/explain.py:162
↓ 1 callers
Function
_build_response_without_perfect_matches
(high_count: int, other_count: int)
services/paper-finder/agents/mabool/api/mabool/agents/common/explain.py:183
↓ 1 callers
Method
_cache_assigned_values
( self, sorted_entities: list[DynamicallyLoadedEntity[DFN]], fields_to_query: set[DFN]
services/paper-finder/libs/dcollection/ai2i/dcollection/caching/cache.py:166
↓ 1 callers
Method
_cache_fetched_data
( self, fetched_entities: list[DynamicallyLoadedEntity[DFN]], fields_to_query: set[DFN
services/paper-finder/libs/dcollection/ai2i/dcollection/caching/cache.py:152
↓ 1 callers
Method
_cache_none_values
( self, sorted_entities: list[DynamicallyLoadedEntity[DFN]], fields_to_query: set[DFN]
services/paper-finder/libs/dcollection/ai2i/dcollection/caching/cache.py:185
↓ 1 callers
Function
_calculate_relevance_criteria_score
Calculate weighted relevance score based on criteria weights (RESTORED from original).
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevance.py:414
↓ 1 callers
Method
_check_pandas_sort
Check if pandas sort method has kind='stable'.
services/paper-finder/dev/python/flake8_plugins/stable_sort_checker.py:25
↓ 1 callers
Method
_checkpoint_excludes_present_or_tracked
(self)
src/core/autoresearch.py:398
↓ 1 callers
Function
_cited_corpus_ids_to_df
(cited_corpus_ids: dict[str, Any])
services/paper-finder/agents/mabool/api/mabool/agents/snowball/snippet_snowball.py:60
↓ 1 callers
Function
_class_signature
(node: ast.ClassDef)
src/core/workspace_manifest.py:271
↓ 1 callers
Function
_classify_role
(rel_path: str)
src/core/workspace_manifest.py:228
↓ 1 callers
Method
_cleanup
()
services/paper-finder/libs/di/ai2i/di/scopes.py:103
↓ 1 callers
Method
_cleanup
()
services/paper-finder/libs/di/ai2i/di/scopes.py:163
↓ 1 callers
Function
_cli
(argv: list[str])
src/core/workspace_manifest.py:1302
↓ 1 callers
Function
_collect_cited_corpus_ids
(doc_collection: DocumentCollection)
services/paper-finder/agents/mabool/api/mabool/agents/snowball/snippet_snowball.py:27
↓ 1 callers
Method
_collect_doc_sources
( self, shortcircuit: Shortcircuit, dense_agent: DenseAgent, snowball_agent: S
services/paper-finder/agents/mabool/api/mabool/agents/complex_search/broad_search.py:132
↓ 1 callers
Method
_compare_properties
( self, parent: ScoreSummary, candidate: ScoreSummary, )
src/core/autoresearch.py:690
↓ 1 callers
Function
_compute_dashboard
Cheap snapshot of progress for the dashboard strip.
src/interactive/web_server.py:161
↓ 1 callers
Function
_compute_document_relevance_score
( doc_id: CorpusId, criterion_judgements: list[RelevanceCriterionJudgement], relevance_criteria: R
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevance.py:348
↓ 1 callers
Function
_convert_relevance_score_to_level
Convert relevance score to 0-3 level (UPDATED to use new threshold constants).
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevance.py:430
↓ 1 callers
Function
_convert_to_relevance_scores
(results: list[LLMJudgementResult], metrics: Metrics)
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevance.py:240
↓ 1 callers
Function
_copy_example_papers
Copy example papers to workspace for reference. The paper writer agent can reference these examples for formatting and language style (b
src/agents/paper_writer.py:146
↓ 1 callers
Function
_copy_paper_writing_resources
Copy shared paper writing resources (command templates) to paper draft directory. Copies the lab's standard LaTeX command templates for math
src/agents/paper_writer.py:118
↓ 1 callers
Function
_copy_paper_writing_templates
Copy paper writing templates (style guide, examples) to workspace. Args: work_dir: Workspace directory
src/agents/paper_writer.py:171
↓ 1 callers
Method
_copy_preserved_paths_to_temp
(self, patterns: Iterable[str])
src/core/autoresearch.py:430
↓ 1 callers
Function
_copy_style_files
Copy LaTeX style files to paper draft directory. The agent runs in a separate workspace without access to neurico's templates, so we cop
src/agents/paper_writer.py:92
↓ 1 callers
Function
_cost_source_files
One cost-bearing file per agent. Mirrors the live-log tailer: prefer the `.jsonl` transcript, fall back to the agent's `.log` (e.g. the paper writ
src/interactive/web_server.py:104
↓ 1 callers
Method
_create_batches
(self)
services/paper-finder/libs/common/ai2i/common/utils/batch.py:64
↓ 1 callers
Function
_create_dynamic_judgement_result_type
(criteria: list[RelevanceCriterion])
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevance.py:158
↓ 1 callers
Function
_create_relevance_judgement_chain
(criteria: list[RelevanceCriterion])
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevance.py:138
↓ 1 callers
Function
_create_retry_logger
()
services/paper-finder/libs/chain/ai2i/chain/builders.py:238
↓ 1 callers
Function
_default_batch_execution_context
()
services/paper-finder/libs/chain/ai2i/chain/endpoints.py:116
↓ 1 callers
Function
_detect_sweep_rollups
Detect groups of >=3 sibling directories with identical file basenames. Common pattern: experiments/sweep/run_001/, run_002/, ... each holdin
src/core/workspace_manifest.py:580
↓ 1 callers
Method
_determine_role
(self, message: BaseMessage)
services/paper-finder/libs/chain/ai2i/chain/gemini/async_genai.py:110
↓ 1 callers
Function
_doc_best_rank
(doc: Document)
services/paper-finder/agents/mabool/api/mabool/agents/complex_search/fast_broad_search.py:167
↓ 1 callers
Function
_document_fields_to_s2_fields
( fields: Sequence[DocumentFieldName], )
services/paper-finder/libs/dcollection/ai2i/dcollection/loaders/s2_rest.py:78
↓ 1 callers
Function
_enrich_anchor_document
(query: str, corpus_id: CorpusId)
services/paper-finder/agents/mabool/api/mabool/agents/paper_finder/anchor_docs.py:27
↓ 1 callers
Function
_enrich_input_with
( input_type: Type[PROMPT_PARAMS], f: Callable[[], Mapping[str, Any]] )
services/paper-finder/libs/chain/ai2i/chain/builders.py:219
↓ 1 callers
Method
_ensure_checkpoint_excludes
(self)
src/core/autoresearch.py:295
↓ 1 callers
Method
_ensure_local_git_identity
(self)
src/core/autoresearch.py:284
↓ 1 callers
Function
_ensure_secret
Mint a Modal secret into a per-experiment env from local env vars. Modal secrets are env-scoped — a secret created in `main` is invisible
templates/skills/modal-training/scripts/lifecycle.py:240
↓ 1 callers
Function
_execute_llm_judgements
( inputs: list[DocumentRelevanceInput], judge_relevance_chain: ChainComputation )
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevance.py:184
↓ 1 callers
Function
_extract_csv_schema
(path: Path)
src/core/workspace_manifest.py:442
↓ 1 callers
Function
_extract_json_object
Pull the first balanced JSON object out of the agent's stdout. Tolerates surrounding prose by scanning for the first '{' and matching braces;
src/agents/manifest_trimmer.py:214
↓ 1 callers
Function
_extract_json_schema
(path: Path)
src/core/workspace_manifest.py:346
↓ 1 callers
Function
_extract_jsonl_schema
(path: Path, max_lines: int = 100)
src/core/workspace_manifest.py:358
↓ 1 callers
Method
_extract_llm_metadata
(self, response: GenerateContentResponse)
services/paper-finder/libs/chain/ai2i/chain/gemini/async_genai.py:128
↓ 1 callers
Function
_extract_markdown_outline
(path: Path)
src/core/workspace_manifest.py:481
↓ 1 callers
Function
_extract_notebook_outline
(path: Path)
src/core/workspace_manifest.py:506
↓ 1 callers
Function
_extract_python_signatures
(path: Path)
src/core/workspace_manifest.py:285
↓ 1 callers
Method
_extract_response_data
(self, response: Any)
services/paper-finder/libs/chain/ai2i/chain/gemini/async_genai.py:118
↓ 1 callers
Method
_extract_text_from_response
(self, response: GenerateContentResponse, llm_output: dict)
services/paper-finder/libs/chain/ai2i/chain/gemini/async_genai.py:168
↓ 1 callers
Method
_extract_usage_metadata
(self, response: GenerateContentResponse)
services/paper-finder/libs/chain/ai2i/chain/gemini/async_genai.py:143
↓ 1 callers
Function
_fallback_curation
Emit a narrow-shape document with explicit fallback markers. The mechanical pass had no agent guidance, so it can't pick primary outputs
src/core/workspace_manifest.py:1272
↓ 1 callers
Method
_fetch_from_doc_sources
( self, doc_sources: SearchIterationSources, docs: DocumentCollection )
services/paper-finder/agents/mabool/api/mabool/agents/complex_search/broad_search.py:214
↓ 1 callers
Method
_fetch_missing_data
( self, query_fn: QueryFnSansContext[DFN], entities_to_query: set[DynamicallyLoadedEnt
services/paper-finder/libs/dcollection/ai2i/dcollection/caching/cache.py:138
↓ 1 callers
Function
_fill_missing_corpus_ids
( docs: list[Document], docs_by_corpus_id: Mapping[CorpusId, Document], found_corpus_ids: Sequence
services/paper-finder/libs/dcollection/ai2i/dcollection/loaders/s2_rest.py:278
↓ 1 callers
Function
_finalize_pending_tasks
( pending_tasks: set[asyncio.Task], session_id: str, is_timeout: bool, is_operative_done: bool, timeout: f
services/paper-finder/agents/mabool/api/mabool/infra/operatives/interaction.py:150
↓ 1 callers
Function
_find_likely_runner_outputs
(file_entries: list[dict])
src/core/workspace_manifest.py:546
↓ 1 callers
Function
_find_relevant_snippet_in_doc
(doc: Document, relevant_snippet: str)
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevant_snippets.py:22
↓ 1 callers
Function
_find_snippet_parts
(text: str, relevant_snippet_parts: list[str])
services/paper-finder/agents/mabool/api/mabool/agents/common/computed_fields/relevant_snippets.py:106
↓ 1 callers
Function
_finish_bootstrap_initial_node_attempt
( *, attempt_dir: Path, work_dir: Path, bootstrap_source_sha: str, child_sha: Optional[str
src/core/autoresearch.py:1411
↓ 1 callers
Function
_flatten
(lst: list[Any])
services/paper-finder/agents/mabool/api/mabool/agents/snowball/snippet_snowball.py:261
↓ 1 callers
Function
_format_for_extension
(ext: str)
src/core/workspace_manifest.py:653
↓ 1 callers
Method
_format_messages
( self, messages: Sequence[BaseMessage] )
services/paper-finder/libs/chain/ai2i/chain/gemini/async_genai.py:80
↓ 1 callers
Function
_gather_files
(paths: List[str], scan_dir: Optional[str])
templates/skills/axiom-lean-prover/scripts/axle_check.py:85
↓ 1 callers
Function
_generate_compute_backend_section
Return proposer-only backend constraints for explicit remote backends.
src/agents/autoresearch_proposer.py:43
↓ 1 callers
Method
_generate_idea_id
Generate a unique ID for an idea. Uses a combination of timestamp and title hash for uniqueness. Args: idea_spe
src/core/idea_manager.py:342
↓ 1 callers
Method
_generate_repo_name
Generate a concise repository name using GPT-4o-mini. Args: title: Research title domain: Research domain (o
src/core/github_manager.py:471
↓ 1 callers
Method
_generate_task_section
Generate the task-specific section of the prompt. This section contains idea-specific details like hypothesis, constraints,
src/templates/prompt_generator.py:309
↓ 1 callers
Function
_get_app_state
(app: FastAPI)
services/paper-finder/libs/di/ai2i/di/integration.py:118
↓ 1 callers
Function
_get_cited_corpus_ids_scores_df
( doc_collection: DocumentCollection, )
services/paper-finder/agents/mabool/api/mabool/agents/snowball/snippet_snowball.py:89
↓ 1 callers
Method
_get_next_batch
(self)
services/paper-finder/libs/dcollection/ai2i/dcollection/loaders/adaptive.py:83
↓ 1 callers
Method
_get_next_batch_size
(self)
services/paper-finder/libs/dcollection/ai2i/dcollection/loaders/adaptive.py:97
↓ 1 callers
Method
_get_next_unloaded_document
(self, origin: Origin)
services/paper-finder/libs/dcollection/ai2i/dcollection/loaders/adaptive.py:106
↓ 1 callers
Function
_glob_to_regex
Translate a POSIX glob with ** support into a regex matching whole paths.
src/core/workspace_manifest.py:184
↓ 1 callers
Function
_handle_inquiry_reply
(query: InquiryReply, session_id: str)
services/paper-finder/agents/mabool/api/mabool/infra/operatives/interaction.py:116
↓ 1 callers
Method
_handle_response
( response: OperativeResponse[BroadSearchOutput], )
services/paper-finder/agents/mabool/api/mabool/agents/complex_search/broad_search.py:304
↓ 1 callers
Method
_handle_sigint
Handle Ctrl+C gracefully.
src/interactive/manager.py:460
↓ 1 callers
Method
_has_next_page
(self)
services/paper-finder/libs/dcollection/ai2i/dcollection/external_api/s2/common.py:101
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