academic-research-skills-codex

Project Url: Imbad0202/academic-research-skills-codex
Introduction: Codex-native Academic Research Skills suite for human-in-the-loop academic research workflows
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Version License: CC BY-NC 4.0 Sponsor

Codex-native packaging of the Academic Research Skills suite. This is the sibling Codex distribution of Academic Research Skills for Claude Code.

This repository vendors the ARS workflow content as a single Codex skill:

skills/academic-research-suite/
  SKILL.md
  manifest.json
  agents/openai.yaml
  ars/
    deep-research/
    academic-paper/
    academic-paper-reviewer/
    academic-pipeline/
    experiment-agent/
    commands/
    hooks/
    docs/
    tests/
    shared/

The original Claude Code ARS checkout is not modified. Upstream content is copied from fresh GitHub clones and adapted through the Codex router in skills/academic-research-suite/SKILL.md.

Claude Code Version

This repository is the Codex package. For the original Claude Code version of Academic Research Skills, use Imbad0202/academic-research-skills.

Use the Claude Code repo when you want the native Claude Code skill layout, Claude-specific agent-team behavior, or the original ARS development history. Use this repo when you want the Codex-native single-suite skill.

Versioning

This Codex package is version 0.1.8. The repo-root VERSION file, skills/academic-research-suite/SKILL.md metadata version, and skills/academic-research-suite/manifest.json adapter_version track the Codex package version independently of the vendored ARS suite. Vendored upstream versions are recorded by commit in manifest.source_repositories[].

Package-level changes are summarized in CHANGELOG.md.

The vendored ARS source currently tracks Imbad0202/academic-research-skills@96b82e82142dc95f117595c207d3e150b078e411 (v3.9.4.2). The v3.9.4.2 upstream delta is CI/release-gate-only under .github/, which this Codex package intentionally excludes; vendored runtime content includes ARS v3.9.4.1 temporal-verification hotfixes and the v3.9.1 through v3.9.4 workflow updates.

Install Or Update

Install the skill from this repo path. Use --method git so public and credentialed GitHub access both work consistently:

python "$HOME/.codex/skills/.system/skill-installer/scripts/install-skill-from-github.py" \
  --repo Imbad0202/academic-research-skills-codex \
  --ref main \
  --path skills/academic-research-suite \
  --method git

To update an existing install:

rm -rf "$HOME/.codex/skills/academic-research-suite"
python "$HOME/.codex/skills/.system/skill-installer/scripts/install-skill-from-github.py" \
  --repo Imbad0202/academic-research-skills-codex \
  --ref main \
  --path skills/academic-research-suite \
  --method git

Open a new Codex conversation after installation. Existing Codex sessions may keep their old skill cache; you do not need to close unrelated Claude or Codex sessions.

Verify with /skills: you should see one ARS entry, academic-research-suite or Academic Research .... You should not see separate academic-paper, academic-pipeline, deep-research, or academic-paper-reviewer skills from this package. If you do, reinstall with the update command above and open a new Codex conversation.

Codex Docs

  • Codex setup covers installation, ars-* aliases, optional tools, Material Passport adapters, and unsupported Claude plugin features.
  • Codex architecture explains the logical ARS pipeline with the Codex runtime overlay.

Usage

Invoke the suite explicitly with $academic-research-suite (singular), then describe the research task and provide any source files, notes, draft text, reviewer comments, or output constraints.

Use $academic-research-suite to help me plan a systematic literature review on
AI adoption in higher education quality assurance.

The Codex adapter routes the request to one of five ARS workflows:

Workflow Use when you need Example prompt
deep-research Research question refinement, literature review, systematic review, meta-analysis, fact-checking Use $academic-research-suite to build a systematic review protocol for AI in higher education QA.
academic-paper Paper outline, drafting, abstract, revision, citation formatting, AI disclosure Use $academic-research-suite to turn these notes into an IMRaD paper outline and drafting plan.
academic-paper-reviewer Manuscript review, simulated peer review, editorial decision, re-review Use $academic-research-suite to review this manuscript and produce a journal-style decision letter.
academic-pipeline End-to-end research-to-paper workflow with integrity gates, review, revision, and final checks Use $academic-research-suite to run an end-to-end research-to-paper pipeline from topic to revised manuscript.
experiment-agent Code experiment planning, human study protocol, statistical interpretation, reproducibility validation Use $academic-research-suite to plan a code experiment and define reproducibility checks.

Claude-Style Aliases

Claude Code v3.7 installs /ars-* slash commands. Codex does not have the same plugin command registry, so this package emulates the command intent inside the single $academic-research-suite skill. Use either form:

Use $academic-research-suite: ars-plan my paper on AI governance in universities.

or, when your Codex client passes slash-prefixed text through as a normal user message:

/ars-plan my paper on AI governance in universities.

If slash input is intercepted by the client, use the plain alias form:

ars-plan my paper on AI governance in universities.
Claude command Codex alias Routed workflow
/ars-plan ars-plan academic-paper plan mode
/ars-outline ars-outline academic-paper outline-only mode
/ars-abstract ars-abstract academic-paper abstract-only mode
/ars-lit-review ars-lit-review academic-paper lit-review mode
/ars-citation-check ars-citation-check academic-paper citation-check mode
/ars-disclosure ars-disclosure academic-paper disclosure mode
/ars-format-convert ars-format-convert academic-paper format-convert mode
/ars-revision-coach ars-revision-coach academic-paper revision-coach mode
/ars-revision ars-revision academic-paper revision mode
/ars-full ars-full academic-pipeline full workflow

Working Pattern

For best results, start with the workflow goal and the current state of your materials:

Use $academic-research-suite.

Goal: write a journal article.
Current materials: I have a literature matrix and rough findings, but no outline.
Output needed now: paper architecture and missing-evidence checklist.
Constraints: English, APA 7, higher education policy audience.

If you only have a paper topic or broad research direction and do not yet have a clear research question, the Codex router should start with ARS Socratic scoping:

Use $academic-research-suite.

I want to write a paper on AI adoption in higher education quality assurance.
I do not yet have a clear research question.
Please use SCR / Socratic dialogue to help me narrow the question first; do not write an outline yet.

Expected route: deep-research socratic mode first. ARS should ask narrowing questions and should not produce an outline or draft until the research question has converged.

For review tasks, provide the manuscript or a path to the manuscript, plus the review mode you want:

Use $academic-research-suite to review this paper.
Mode: full review.
Focus: methodology, contribution, citation integrity, and likely desk-reject risks.
Output: reviewer reports plus editorial decision letter.

For staged pipelines, ask for a checkpoint instead of asking Codex to run the entire process silently:

Use $academic-research-suite to start an academic-pipeline run.
Begin with Stage 0 intake and stop after producing the pipeline dashboard.

Smoke Tests

In a new Codex conversation:

/skills

Expected: one ARS entry only.

Then test Socratic routing:

Use $academic-research-suite.
I want to write a paper on AI adoption in higher education quality assurance.
I do not yet have a clear research question.

Expected: route to deep-research socratic mode and ask narrowing questions.

CLI smoke test:

codex exec --ephemeral --sandbox read-only \
  -C /path/to/academic-research-skills-codex \
  'Use $academic-research-suite. Router smoke test only. User request to classify: I want to write a paper on AI adoption in higher education quality assurance, but I do not yet have a clear research question. According to the academic-research-suite router, classify the workflow and mode.'

Non-Blocking Codex Warnings

These Codex messages do not mean ARS failed to install:

  • [features].codex_hooks is deprecated — update your Codex config when convenient; ARS Codex does not require hooks for normal use.
  • hooks need review before they can run — review those hooks separately if you use them. ARS Codex treats vendored Claude hooks as traceability metadata and does not require them.

Codex Adapter Behavior

ARS was originally written for Claude Code. In this Codex package:

  • The vendored agents/*.md files are used as role and phase prompts.
  • The vendored commands/ars-*.md files are prompt recipes only. Codex does not register them as slash commands.
  • The vendored hooks/hooks.json file is preserved for upstream traceability only. Codex does not install Claude Code hooks from this package.
  • Codex does not automatically spawn background agents unless you explicitly ask for delegated or parallel agent work.
  • Web/source verification uses Codex browsing and must cite sources when current or external facts matter.
  • Cross-model verification is disabled by default. When explicitly requested in this Codex package, configure ARS_CROSS_MODEL=claude-opus-4.7 and ANTHROPIC_API_KEY; the external reviewer uses Anthropic Claude Opus 4.7 API, not Codex/OpenAI API. Upstream GPT/Gemini secondary-dispatch instructions are ignored unless this explicit Anthropic configuration is present.
  • Upstream references to a "fresh Claude Code session" mean a new Codex conversation in this package; Material Passport reset semantics still apply.
  • If a citation, source, statistic, or journal policy cannot be verified, Codex should mark it as unverified rather than invent support.

ARS v3.9.4.2 Parity

This package aims for the same user-facing workflow content as upstream ARS v3.9.4.2 where Codex has an equivalent concept.

Upstream ARS feature Codex package behavior
One installable plugin One installable Codex skill at skills/academic-research-suite
/ars-* slash commands Emulated as ars-* aliases through the skill router; not native slash commands
Four upstream skills auto-discovered from skills/ symlinks Single Codex router skill selects the workflow and reads the vendored workflow WORKFLOW.md files
Plugin-shipped agents Agent files are role/phase prompts; Codex runs them inline unless the user explicitly asks for delegated subagents
model: opus / model: sonnet command routing Treated as Claude metadata; Codex uses the active model
SessionStart and SubagentStop hooks Vendored for traceability only; Codex does not install or execute Claude hooks
Plugin marketplace update / auto-update Not available here; update by reinstalling or pulling this Codex repo
Claude Code Agent Team Not automatic; Codex subagents require an explicit user request for delegation or parallel agents
Cross-model GPT/Gemini dispatch from upstream docs Disabled; Codex package only supports optional Anthropic Claude Opus 4.7 review when explicitly configured

Optional Claude Opus 4.7 Reviewer API

For reviewer calibration or cross-model devil's advocate checks:

export ANTHROPIC_API_KEY="<your-anthropic-api-key>"
export ARS_CROSS_MODEL="claude-opus-4.7"

Then ask for cross-model verification explicitly in the prompt. Without both environment variables, ARS Codex falls back to single-runtime review and should report that the Claude Opus 4.7 verifier was unavailable.

Support And Sponsorship

If ARS Codex helps your research workflow, you can support maintenance through Buy Me a Coffee.

Security

Do not open public issues for vulnerabilities. Follow SECURITY.md for private reporting, and see the release readiness and security report for the latest local validation summary.

File Layout For Advanced Use

The entry point is:

skills/academic-research-suite/SKILL.md

Workflow content is under:

skills/academic-research-suite/ars/<workflow>/

Shared schemas, compliance rules, and cross-workflow contracts are under:

skills/academic-research-suite/ars/shared/

When debugging or updating the package, preserve these paths. Many ARS workflow files cross-reference shared/, scripts/, examples/, and other workflow directories.

Update Policy

Updates sync selected upstream ARS content into skills/academic-research-suite/ars/. Do not mirror the Claude Code repo blindly; exclude Claude/plugin loader files such as .claude/, .claude-plugin/, .github/, source .gitignore, and symlink-only alias directories that are not needed in Codex.

Inactive Upstream Scripts

Some upstream maintenance scripts are vendored but intentionally inactive in this Codex package because they require non-vendored Claude Code inputs such as .claude/CLAUDE.md. See inactive_upstream_scripts in skills/academic-research-suite/manifest.json before wiring any upstream script into Codex CI.

Contributors And Acknowledgements

Cheng-I Wu - Maintainer of the ARS suite and this Codex sibling distribution.

Codex - Assisted with the Codex adapter packaging, router-policy hardening, test fixes, and release-readiness review under maintainer direction.

Vendored upstream ARS contributors are acknowledged in skills/academic-research-suite/ars/README.md.

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