research-e-coding

name	research[E]-coding
description	ResearchPilot Research Assistant [Phase E]: Coding
version	2.0.0
license	LICENSE

user_requirements.md priority: All user constraints recorded in docs/user_requirements.md (direction preferences, implementation requirements, document format, etc.) take precedence over any default instruction in this skill. Always read that file before generating any output to ensure compliance with confirmed user constraints.

Phase E: Coding

Implement code file by file according to docs/implementation.md, maintain the development log, and conduct a proactive code review (runnable + logically correct) when all files are complete.

Prerequisite: docs/implementation.md exists and the pre-coding checklist (Phase D end) has been completed.

Workflow Overview & Outputs

ResearchPilot-Skills splits a complete academic research project into seven independent stage skills. The current skill is one link in that chain.

Seven-Stage Chain

Skill	Phase	Main Output
/research[A]-exploration	Direction Exploration	docs/idea_report.md Part 1
/research[B]-idea	Idea Deepening	docs/idea_report.md Part 2
/research[C]-experiment	Experiment Design	docs/idea_report.md Part 3
/research[D]-implementation	Implementation Design	docs/implementation.md
/research[E]-coding	Coding	code/ + docs/dev_log.md
/research[F]-iteration	Code Iteration	dev_log.md iteration records
/research[G.0]-plan	Paper Planning	manuscript architecture + notebooks/figures.ipynb
/research[G.1]-method	Method	manuscript Method section
/research[G.2]-experiments	Experiments	manuscript Experiments section
/research[G.3]-abstract	Abstract	manuscript Abstract
/research[G.4]-introduction	Introduction	manuscript Introduction
/research[G.5]-related	Related Works	manuscript Related Works
/research[G.6]-conclusion	Conclusion + References	manuscript Conclusion
/research[G.7]-review	Full-paper Review	review report

Project Directory Structure

docs/
  idea_report.md        # Research report in three parts:
                        #   Part 1: Motivation, RQs, Key Works  (Phase A)
                        #   Part 2: Introduction, Related Works, Method  (Phase B)
                        #   Part 3: Datasets, Experiment Design, Resource Estimate  (Phase C)
  implementation.md     # Coding guide: file- and function-level implementation plan  (Phase D)
  dev_log.md            # Dev log: progress, decisions, "How to Run" section  (Phase E)
  user_requirements.md  # User constraints: collected and maintained by Claude
  papers/               # Downloaded paper PDFs or abstract TXTs
  manuscripts/          # Paper drafts, each revision archived separately
                        #   (e.g. v1.0-initial-draft.md, v1.1-revision.md)

code/
  src/                  # Core model and training code
  scripts/              # Run scripts (train.sh, evaluate.sh, ablation.sh)
  configs/              # Hyperparameter config files
  baselines/            # Baseline model implementations
  notebooks/            # Visualization notebooks; paper figure/table generation
  data/                 # Datasets (gitignored)
  results/              # Experiment results (gitignored)
  logs/                 # Training logs (gitignored)
  README.md             # Environment setup and run commands
  requirements.txt      # Dependencies (library names only, no torch family)

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Command

/research[E]-coding

An optional natural-language instruction may follow the command. The AI will treat it as an additional constraint or supplement for this invocation.

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Phase E Flow Overview

E-0 Create README.md and notebooks/ directory
E-1 Create dev_log.md (with progress table and "How to Run" chapter)
E-2 Implement files in the order specified by implementation.md
    After each file: update dev_log.md + update README.md if needed + add notebook
    After each module: validate consistency with implementation.md
E-3 requirements.txt rules (library names only, no versions, no torch family)
E-4 Design issue found → pause and inform user, do not work around it
E-5 implementation.md error found → fix the document first, then fix the code
E-6 Post-file sync (README + "How to Run" chapter in dev_log.md)
E-7 Proactive code review after all files complete
E-8 Poor experiment results → backtrack through B/C/D (no code-only patches)

Full step-by-step instructions: references/phase-E.md.

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dev_log.md Rules

• Updated in sync with each completed file — no batch updates
• Has a fixed "How to Run" chapter at the bottom; every code change must automatically check whether this chapter needs updating
• ✅ Done can only be marked after a file is written and runs without errors

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Non-Negotiable Constraints

1. requirements.txt must not contain torch, torchvision, or torchaudio.
2. dev_log.md must be updated with each file — no batch catch-up writes.
3. When design is found to be unworkable, confirm the backtracking scope with the user and re-walk the corresponding Phase B/C/D flow — never patch around it in code only.
4. After every code change, automatically judge whether the "How to Run" chapter in dev_log.md needs to be updated.
5. Rules in references/template-flexibility.md take precedence over any specific template instruction.

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On Phase Completion

After the code review passes:

Phase E complete. Code review passed — code is runnable and logically
consistent with the design.

→ Use `/research[F]-paper` to start paper writing.

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Reference Files

• Detailed flow: references/phase-E.md
• Template flexibility rules: references/template-flexibility.md