Hypothesis proximity update
Skill panjose/Co-Scientist/skills/hypothesis-proximity-update
Scientific agent skills for Claude Code and Codex that turn research goals into auditable hypothesis generation, review, ranking, evolution, and synthesis.
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Update hypothesis proximity state by invoking the canonical embedding bridge for one hypothesis.
SKILL.md
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hypothesis-proximity-update
Goal:
- Update hypothesis proximity state by invoking the canonical embedding bridge for one hypothesis.
Inputs:
- optional existing
state/PROXIMITY_GRAPH.json - target
hypothesis_id - run-frozen embedding provider settings from
state/RESOLVED_RUN_CONFIG.json
Outputs:
- updated
state/proximity_receipts/<hypothesis_id>.json - updated
state/PROXIMITY_STATUS.json - updated in-memory
ProximityGraphContract - updated
state/PROXIMITY_GRAPH.jsonwhen the provider returns a valid embedding - updated
state/PIPELINE_STATE.json - updated
state/CURRENT_STAGE.json
Context Loading:
- Open
skills/shared-references/schema-index.md. - Read
packages/agent_contracts/state.pyand confirm the exactProximityGraphContractshape before writingstate/PROXIMITY_GRAPH.json. - Read
packages/agent_contracts/proximity.pyand confirm the proximity receipt and status schemas before interpreting provider outcomes. - Read
packages/agent_contracts/pipeline_runtime.pybefore updatingstate/PIPELINE_STATE.jsonorstate/CURRENT_STAGE.json. - Load the current proximity graph if it exists. If it does not exist yet, start from an empty
ProximityGraphContract. - Treat embedding generation as a bridge/tool concern. Host agents must not generate, infer, paste, or hand-write numeric embeddings in prompt output.
- Do not skip this skill merely because no embedding vector is already present in the execution context.
Execution Contract:
- This skill is deterministic and must not call an LLM.
- Use
from tools import sync_pipeline_stage_artifactsas the canonical paired write surface for entering theProximitysubstage. - On entry, call
tools.sync_pipeline_stage_artifacts(run_dir, current_phase="Proximity", current_skill="hypothesis-proximity-update"). - Use
from tools import update_hypothesis_proximityas the stable invocation surface. - The exported bridge is implemented in
packages/agent_mechanics/hypothesis_embedding.py. - The canonical hypothesis-to-embedding text formatter is implemented in
packages/agent_mechanics/hypothesis_embedding_text.py. - The helper signature is
update_hypothesis_proximity(run_dir, hypothesis_id, config=None, provider=None) -> ProximityEmbeddingReceiptContract. - The bridge formats the hypothesis text, reads the run-frozen proximity provider settings from
state/RESOLVED_RUN_CONFIG.jsonunless an explicit test config is passed, calls the configured provider when enabled, records a proximity receipt/status, and updatesstate/PROXIMITY_GRAPH.jsononly when a valid embedding is returned. - Provider-specific backends such as
openai_compatibleandgeminimust remain behindtools.update_hypothesis_proximity(...); host agents must not call provider SDKs directly or paste provider-returned vectors into artifacts. - The lower-level graph helper remains
tools.update_proximity_graph(...), implemented inpackages/agent_mechanics/proximity_update.py; host agents must not call it with prompt-fabricated vectors. - This skill must not hand-write embeddings, infer embeddings from hypothesis prose, or fabricate placeholder numeric vectors.
- If the provider is disabled, unavailable, invalid, or fails, preserve the bridge-written receipt/status, do not fabricate a graph update, and return control to ranking with receipt-gated fallback semantics.
Execution Steps:
- Open
skills/shared-references/schema-index.md, then readpackages/agent_contracts/state.py,packages/agent_contracts/proximity.py, andpackages/agent_contracts/pipeline_runtime.pybefore writing proximity or run-level stage artifacts. - Before running the bridge, call
tools.sync_pipeline_stage_artifacts(run_dir, current_phase="Proximity", current_skill="hypothesis-proximity-update"). - Confirm the target
hypothesis_ididentifies an existing canonicalhypotheses/<id>/HYPOTHESIS.jsonartifact. - Call
tools.update_hypothesis_proximity(run_dir, hypothesis_id)exactly once for the target hypothesis. - Inspect the returned
ProximityEmbeddingReceiptContractand the persistedstate/proximity_receipts/<hypothesis_id>.json. - If the receipt status is
succeeded, validate the updatedstate/PROXIMITY_GRAPH.json. - If the receipt status is
skipped_disabled,skipped_provider_unavailable,failed_provider_error, orfailed_invalid_embedding, preserve the receipt/status and return control to ranking. Do not infer or fabricate placeholder embeddings from text, IDs, or manual feature heuristics. - Validate the updated receipt/status artifacts before declaring completion.
Artifact Rules:
state/PROXIMITY_GRAPH.jsonmust remain the canonical persisted graph artifact.state/proximity_receipts/<hypothesis_id>.jsonis the canonical per-hypothesis embedding bridge receipt.state/PROXIMITY_STATUS.jsonis the canonical run-level proximity bridge status artifact.- Similarity edges must stay symmetric across both hypothesis IDs.
- Each persisted graph embedding should include metadata for provider, model, dimensions, input text hash, and embedding config hash.
- If the graph already contains the target hypothesis ID with the same embedding input hash and embedding config hash, the bridge may confirm the existing state through a
succeededreceipt withgraph_updated=false; do not duplicate entries. - If the graph already contains the target hypothesis ID with different or missing input/config metadata, preserve the bridge receipt and do not overwrite the existing embedding in prompt code.
- Placeholder embeddings, manually engineered stand-in vectors, or prose-derived pseudo-embeddings must never be written into the canonical graph artifact.
Completion Rule:
- This skill is complete only when
tools.update_hypothesis_proximity(run_dir, hypothesis_id)has returned a persisted receipt and eitherstate/PROXIMITY_GRAPH.jsonvalidates after asucceededreceipt or the receipt/status explicitly records why the graph was not updated.