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NanoResearch — Codex Integration Mode

NanoResearch is an end-to-end autonomous AI research engine. In Codex integration mode, Codex should drive the existing pipeline rather than inventing a second workflow.

Core Goal

Given a research topic, NanoResearch should produce a resumable research workspace containing:

  • literature artifacts
  • planning artifacts
  • runnable experiment code when needed
  • execution or literature-analysis evidence
  • figures
  • a LaTeX paper draft
  • review output and final exported assets

Pipeline

NanoResearch uses a 9-stage pipeline:

IDEATION -> PLANNING -> SETUP -> CODING -> EXECUTION -> ANALYSIS -> FIGURE_GEN -> WRITING -> REVIEW

Stage meanings:

  • ideation: literature search, gap finding, hypothesis or theme extraction
  • planning: experiment blueprint or survey blueprint generation
  • setup: environment and resource preparation
  • coding: runnable experiment generation
  • execution: local or SLURM-backed experiment execution
  • analysis: structured evidence extraction from outputs
  • figure_gen: figure generation for paper assets
  • writing: LaTeX paper drafting
  • review: critique, verification, and revision

Workspace Convention

Workspaces live under ~/.nanoresearch/workspace/research/. A typical workspace contains:

{session_dir}/
├── manifest.json
├── papers/
├── plans/
├── experiment/
├── drafts/
├── figures/
├── output/
└── logs/

Reuse an existing workspace when the user asks to continue, inspect status, resume, or revise a prior run.

Paper Modes

Topic prefixes:

  • original: Topic -> original_research
  • survey:short: Topic -> survey_short
  • survey:standard: Topic -> survey_standard
  • survey:long: Topic -> survey_long

Behavior:

  • original research follows the full 9-stage pipeline
  • survey modes skip experiment-heavy stages and use literature-grounded planning, writing, and review
  • the prefix is parsed by the existing CLI and manifest logic; Codex should reuse that behavior

Codex Intent Mapping

If the user asks for... Codex should interpret it as... Preferred repo entry / behavior
full research run topic-to-paper pipeline nanoresearch run --topic "..." or the equivalent workspace-driven pipeline flow
ideation or literature survey stage 1 ideation produce papers/ideation_output.json in a workspace
planning stage 2 planning produce plans/experiment_blueprint.json or plans/survey_blueprint.json
experiment execution setup + coding + execution use the existing experiment path for original research
analysis stage 6 evidence extraction produce plans/analysis_output.json
writing figure generation + paper drafting produce or update paper outputs in the workspace
review review + revision pass produce or update drafts/review_output.json and revised paper assets
status inspect the active workspace read and normalize manifest.json
resume continue an interrupted run restart from the first non-completed stage

Grounding Rules

  • never fabricate experiment results
  • never fabricate citations
  • prefer existing CLI / orchestrator behavior over ad hoc scripts
  • keep paper claims tied to actual outputs or verified literature
  • preserve checkpoint and resume semantics via manifest.json

Codex Operating Rules

  1. Prefer the existing NanoResearch CLI or Python entrypoints when driving the system.
  2. Do not introduce a separate Codex-specific pipeline mode.
  3. Keep outputs compatible with existing workspaces and manifests.
  4. Never fabricate results or citations.
  5. When a user asks for pipeline work, operate through the existing workspace artifacts and stage boundaries described above.