[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"project-76080":3},{"id":4,"name":5,"fullName":6,"owner":7,"repo":5,"description":8,"homepage":9,"htmlUrl":10,"language":11,"languages":10,"totalLinesOfCode":10,"stars":12,"forks":13,"watchers":14,"openIssues":15,"contributorsCount":16,"subscribersCount":16,"size":16,"stars1d":17,"stars7d":18,"stars30d":19,"stars90d":16,"forks30d":16,"starsTrendScore":20,"compositeScore":21,"rankGlobal":10,"rankLanguage":10,"license":22,"archived":23,"fork":23,"defaultBranch":24,"hasWiki":23,"hasPages":23,"topics":25,"createdAt":10,"pushedAt":10,"updatedAt":36,"readmeContent":37,"aiSummary":38,"trendingCount":16,"starSnapshotCount":16,"syncStatus":39,"lastSyncTime":40,"discoverSource":41},76080,"academic-research-skills-codex","Imbad0202\u002Facademic-research-skills-codex","Imbad0202","Codex-native Academic Research Skills suite for human-in-the-loop academic research workflows","https:\u002F\u002Fgithub.com\u002FImbad0202\u002Facademic-research-skills",null,"Python",3558,200,7,1,0,492,1184,2958,1476,108.91,"Other",false,"main",[26,27,28,29,30,31,32,33,34,35],"academic-pipeline","academic-research","academic-writing","ai-research","codex","literature-review","openai-codex","peer-review","prompt-engineering","research-assistant","2026-06-12 04:01:20","# Academic Research Skills for Codex\n\n[![Version](https:\u002F\u002Fimg.shields.io\u002Fbadge\u002Fversion-v0.1.8-blue)](VERSION)\n[![License: CC BY-NC 4.0](https:\u002F\u002Fimg.shields.io\u002Fbadge\u002Flicense-CC%20BY--NC%204.0-lightgrey)](https:\u002F\u002Fcreativecommons.org\u002Flicenses\u002Fby-nc\u002F4.0\u002F)\n[![Sponsor](https:\u002F\u002Fimg.shields.io\u002Fbadge\u002Fsponsor-Buy%20Me%20a%20Coffee-orange?logo=buy-me-a-coffee)](https:\u002F\u002Fbuymeacoffee.com\u002Fcrucify020v)\n\nCodex-native packaging of the Academic Research Skills suite. This is the\nsibling Codex distribution of\n[Academic Research Skills for Claude Code](https:\u002F\u002Fgithub.com\u002FImbad0202\u002Facademic-research-skills).\n\nThis repository vendors the ARS workflow content as a single Codex skill:\n\n```text\nskills\u002Facademic-research-suite\u002F\n  SKILL.md\n  manifest.json\n  agents\u002Fopenai.yaml\n  ars\u002F\n    deep-research\u002F\n    academic-paper\u002F\n    academic-paper-reviewer\u002F\n    academic-pipeline\u002F\n    experiment-agent\u002F\n    commands\u002F\n    hooks\u002F\n    docs\u002F\n    tests\u002F\n    shared\u002F\n```\n\nThe original Claude Code ARS checkout is not modified. Upstream content is copied\nfrom fresh GitHub clones and adapted through the Codex router in\n`skills\u002Facademic-research-suite\u002FSKILL.md`.\n\n## Claude Code Version\n\nThis repository is the Codex package. For the original Claude Code version of\nAcademic Research Skills, use\n[Imbad0202\u002Facademic-research-skills](https:\u002F\u002Fgithub.com\u002FImbad0202\u002Facademic-research-skills).\n\nUse the Claude Code repo when you want the native Claude Code skill layout,\nClaude-specific agent-team behavior, or the original ARS development history.\nUse this repo when you want the Codex-native single-suite skill.\n\n## Versioning\n\nThis Codex package is version `0.1.8`. The repo-root `VERSION` file,\n`skills\u002Facademic-research-suite\u002FSKILL.md` metadata version, and\n`skills\u002Facademic-research-suite\u002Fmanifest.json` `adapter_version` track the\nCodex package version independently of the vendored ARS suite. Vendored upstream\nversions are recorded by commit in `manifest.source_repositories[]`.\n\nPackage-level changes are summarized in [`CHANGELOG.md`](CHANGELOG.md).\n\nThe vendored ARS source currently tracks\n`Imbad0202\u002Facademic-research-skills@96b82e82142dc95f117595c207d3e150b078e411`\n(`v3.9.4.2`). The v3.9.4.2 upstream delta is CI\u002Frelease-gate-only under\n`.github\u002F`, which this Codex package intentionally excludes; vendored runtime\ncontent includes ARS v3.9.4.1 temporal-verification hotfixes and the v3.9.1\nthrough v3.9.4 workflow updates.\n\n## Install Or Update\n\nInstall the skill from this repo path. Use `--method git` so public and\ncredentialed GitHub access both work consistently:\n\n```bash\npython \"$HOME\u002F.codex\u002Fskills\u002F.system\u002Fskill-installer\u002Fscripts\u002Finstall-skill-from-github.py\" \\\n  --repo Imbad0202\u002Facademic-research-skills-codex \\\n  --ref main \\\n  --path skills\u002Facademic-research-suite \\\n  --method git\n```\n\nTo update an existing install:\n\n```bash\nrm -rf \"$HOME\u002F.codex\u002Fskills\u002Facademic-research-suite\"\npython \"$HOME\u002F.codex\u002Fskills\u002F.system\u002Fskill-installer\u002Fscripts\u002Finstall-skill-from-github.py\" \\\n  --repo Imbad0202\u002Facademic-research-skills-codex \\\n  --ref main \\\n  --path skills\u002Facademic-research-suite \\\n  --method git\n```\n\nOpen a new Codex conversation after installation. Existing Codex sessions may\nkeep their old skill cache; you do not need to close unrelated Claude or Codex\nsessions.\n\nVerify with `\u002Fskills`: you should see one ARS entry, `academic-research-suite`\nor `Academic Research ...`. You should **not** see separate `academic-paper`,\n`academic-pipeline`, `deep-research`, or `academic-paper-reviewer` skills from\nthis package. If you do, reinstall with the update command above and open a new\nCodex conversation.\n\n## Codex Docs\n\n- [Codex setup](skills\u002Facademic-research-suite\u002Fars\u002Fdocs\u002FSETUP.md) covers\n  installation, `ars-*` aliases, optional tools, Material Passport adapters,\n  and unsupported Claude plugin features.\n- [Codex architecture](skills\u002Facademic-research-suite\u002Fars\u002Fdocs\u002FARCHITECTURE.md)\n  explains the logical ARS pipeline with the Codex runtime overlay.\n\n## Usage\n\nInvoke the suite explicitly with `$academic-research-suite` (singular), then\ndescribe the research task and provide any source files, notes, draft text,\nreviewer comments, or output constraints.\n\n```text\nUse $academic-research-suite to help me plan a systematic literature review on\nAI adoption in higher education quality assurance.\n```\n\nThe Codex adapter routes the request to one of five ARS workflows:\n\n| Workflow | Use when you need | Example prompt |\n|---|---|---|\n| `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.` |\n| `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.` |\n| `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.` |\n| `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.` |\n| `experiment-agent` | Code experiment planning, human study protocol, statistical interpretation, reproducibility validation | `Use $academic-research-suite to plan a code experiment and define reproducibility checks.` |\n\n### Claude-Style Aliases\n\nClaude Code v3.7 installs `\u002Fars-*` slash commands. Codex does not have the same\nplugin command registry, so this package emulates the command intent inside the\nsingle `$academic-research-suite` skill. Use either form:\n\n```text\nUse $academic-research-suite: ars-plan my paper on AI governance in universities.\n```\n\nor, when your Codex client passes slash-prefixed text through as a normal user\nmessage:\n\n```text\n\u002Fars-plan my paper on AI governance in universities.\n```\n\nIf slash input is intercepted by the client, use the plain alias form:\n\n```text\nars-plan my paper on AI governance in universities.\n```\n\n| Claude command | Codex alias | Routed workflow |\n|---|---|---|\n| `\u002Fars-plan` | `ars-plan` | `academic-paper` `plan` mode |\n| `\u002Fars-outline` | `ars-outline` | `academic-paper` `outline-only` mode |\n| `\u002Fars-abstract` | `ars-abstract` | `academic-paper` `abstract-only` mode |\n| `\u002Fars-lit-review` | `ars-lit-review` | `academic-paper` `lit-review` mode |\n| `\u002Fars-citation-check` | `ars-citation-check` | `academic-paper` `citation-check` mode |\n| `\u002Fars-disclosure` | `ars-disclosure` | `academic-paper` `disclosure` mode |\n| `\u002Fars-format-convert` | `ars-format-convert` | `academic-paper` `format-convert` mode |\n| `\u002Fars-revision-coach` | `ars-revision-coach` | `academic-paper` `revision-coach` mode |\n| `\u002Fars-revision` | `ars-revision` | `academic-paper` `revision` mode |\n| `\u002Fars-full` | `ars-full` | `academic-pipeline` full workflow |\n\n### Working Pattern\n\nFor best results, start with the workflow goal and the current state of your\nmaterials:\n\n```text\nUse $academic-research-suite.\n\nGoal: write a journal article.\nCurrent materials: I have a literature matrix and rough findings, but no outline.\nOutput needed now: paper architecture and missing-evidence checklist.\nConstraints: English, APA 7, higher education policy audience.\n```\n\nIf you only have a paper topic or broad research direction and do not yet have a\nclear research question, the Codex router should start with ARS Socratic\nscoping:\n\n```text\nUse $academic-research-suite.\n\nI want to write a paper on AI adoption in higher education quality assurance.\nI do not yet have a clear research question.\nPlease use SCR \u002F Socratic dialogue to help me narrow the question first; do not write an outline yet.\n```\n\nExpected route: `deep-research` `socratic` mode first. ARS should ask narrowing\nquestions and should not produce an outline or draft until the research question\nhas converged.\n\nFor review tasks, provide the manuscript or a path to the manuscript, plus the\nreview mode you want:\n\n```text\nUse $academic-research-suite to review this paper.\nMode: full review.\nFocus: methodology, contribution, citation integrity, and likely desk-reject risks.\nOutput: reviewer reports plus editorial decision letter.\n```\n\nFor staged pipelines, ask for a checkpoint instead of asking Codex to run the\nentire process silently:\n\n```text\nUse $academic-research-suite to start an academic-pipeline run.\nBegin with Stage 0 intake and stop after producing the pipeline dashboard.\n```\n\n### Smoke Tests\n\nIn a new Codex conversation:\n\n```text\n\u002Fskills\n```\n\nExpected: one ARS entry only.\n\nThen test Socratic routing:\n\n```text\nUse $academic-research-suite.\nI want to write a paper on AI adoption in higher education quality assurance.\nI do not yet have a clear research question.\n```\n\nExpected: route to `deep-research` `socratic` mode and ask narrowing questions.\n\nCLI smoke test:\n\n```bash\ncodex exec --ephemeral --sandbox read-only \\\n  -C \u002Fpath\u002Fto\u002Facademic-research-skills-codex \\\n  '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.'\n```\n\n### Non-Blocking Codex Warnings\n\nThese Codex messages do not mean ARS failed to install:\n\n- `[features].codex_hooks is deprecated` — update your Codex config when\n  convenient; ARS Codex does not require hooks for normal use.\n- `hooks need review before they can run` — review those hooks separately if\n  you use them. ARS Codex treats vendored Claude hooks as traceability metadata\n  and does not require them.\n\n### Codex Adapter Behavior\n\nARS was originally written for Claude Code. In this Codex package:\n\n- The vendored `agents\u002F*.md` files are used as role and phase prompts.\n- The vendored `commands\u002Fars-*.md` files are prompt recipes only. Codex does not\n  register them as slash commands.\n- The vendored `hooks\u002Fhooks.json` file is preserved for upstream traceability\n  only. Codex does not install Claude Code hooks from this package.\n- Codex does not automatically spawn background agents unless you explicitly ask\n  for delegated or parallel agent work.\n- Web\u002Fsource verification uses Codex browsing and must cite sources when current\n  or external facts matter.\n- Cross-model verification is disabled by default. When explicitly requested in\n  this Codex package, configure `ARS_CROSS_MODEL=claude-opus-4.7` and\n  `ANTHROPIC_API_KEY`; the external reviewer uses Anthropic Claude Opus 4.7 API,\n  not Codex\u002FOpenAI API. Upstream GPT\u002FGemini secondary-dispatch instructions are\n  ignored unless this explicit Anthropic configuration is present.\n- Upstream references to a \"fresh Claude Code session\" mean a new Codex\n  conversation in this package; Material Passport reset semantics still apply.\n- If a citation, source, statistic, or journal policy cannot be verified, Codex\n  should mark it as unverified rather than invent support.\n\n### ARS v3.9.4.2 Parity\n\nThis package aims for the same user-facing workflow content as upstream ARS\nv3.9.4.2 where Codex has an equivalent concept.\n\n| Upstream ARS feature | Codex package behavior |\n|---|---|\n| One installable plugin | One installable Codex skill at `skills\u002Facademic-research-suite` |\n| `\u002Fars-*` slash commands | Emulated as `ars-*` aliases through the skill router; not native slash commands |\n| Four upstream skills auto-discovered from `skills\u002F` symlinks | Single Codex router skill selects the workflow and reads the vendored workflow `WORKFLOW.md` files |\n| Plugin-shipped agents | Agent files are role\u002Fphase prompts; Codex runs them inline unless the user explicitly asks for delegated subagents |\n| `model: opus` \u002F `model: sonnet` command routing | Treated as Claude metadata; Codex uses the active model |\n| SessionStart and SubagentStop hooks | Vendored for traceability only; Codex does not install or execute Claude hooks |\n| Plugin marketplace update \u002F auto-update | Not available here; update by reinstalling or pulling this Codex repo |\n| Claude Code Agent Team | Not automatic; Codex subagents require an explicit user request for delegation or parallel agents |\n| Cross-model GPT\u002FGemini dispatch from upstream docs | Disabled; Codex package only supports optional Anthropic Claude Opus 4.7 review when explicitly configured |\n\n### Optional Claude Opus 4.7 Reviewer API\n\nFor reviewer calibration or cross-model devil's advocate checks:\n\n```bash\nexport ANTHROPIC_API_KEY=\"\u003Cyour-anthropic-api-key>\"\nexport ARS_CROSS_MODEL=\"claude-opus-4.7\"\n```\n\nThen ask for cross-model verification explicitly in the prompt. Without both\nenvironment variables, ARS Codex falls back to single-runtime review and should\nreport that the Claude Opus 4.7 verifier was unavailable.\n\n## Support And Sponsorship\n\nIf ARS Codex helps your research workflow, you can support maintenance through\n[Buy Me a Coffee](https:\u002F\u002Fbuymeacoffee.com\u002Fcrucify020v).\n\n## Security\n\nDo not open public issues for vulnerabilities. Follow\n[`SECURITY.md`](SECURITY.md) for private reporting, and see the\n[release readiness and security report](security_best_practices_report.md) for\nthe latest local validation summary.\n\n### File Layout For Advanced Use\n\nThe entry point is:\n\n```text\nskills\u002Facademic-research-suite\u002FSKILL.md\n```\n\nWorkflow content is under:\n\n```text\nskills\u002Facademic-research-suite\u002Fars\u002F\u003Cworkflow>\u002F\n```\n\nShared schemas, compliance rules, and cross-workflow contracts are under:\n\n```text\nskills\u002Facademic-research-suite\u002Fars\u002Fshared\u002F\n```\n\nWhen debugging or updating the package, preserve these paths. Many ARS workflow\nfiles cross-reference `shared\u002F`, `scripts\u002F`, `examples\u002F`, and other workflow\ndirectories.\n\n## Update Policy\n\nUpdates sync selected upstream ARS content into `skills\u002Facademic-research-suite\u002Fars\u002F`.\nDo not mirror the Claude Code repo blindly; exclude Claude\u002Fplugin loader files\nsuch as `.claude\u002F`, `.claude-plugin\u002F`, `.github\u002F`, source `.gitignore`, and\nsymlink-only alias directories that are not needed in Codex.\n\n### Inactive Upstream Scripts\n\nSome upstream maintenance scripts are vendored but intentionally inactive in\nthis Codex package because they require non-vendored Claude Code inputs such as\n`.claude\u002FCLAUDE.md`. See `inactive_upstream_scripts` in\n`skills\u002Facademic-research-suite\u002Fmanifest.json` before wiring any upstream script\ninto Codex CI.\n\n## Contributors And Acknowledgements\n\n**Cheng-I Wu** - Maintainer of the ARS suite and this Codex sibling\ndistribution.\n\n**Codex** - Assisted with the Codex adapter packaging, router-policy hardening,\ntest fixes, and release-readiness review under maintainer direction.\n\nVendored upstream ARS contributors are acknowledged in\n[`skills\u002Facademic-research-suite\u002Fars\u002FREADME.md`](skills\u002Facademic-research-suite\u002Fars\u002FREADME.md#contributors).\n","academic-research-skills-codex 是一个专为学术研究工作流程设计的Codex原生技能套件，旨在辅助人类在循环中的学术研究。其核心功能包括文献回顾、学术论文撰写与审阅、实验设计等，并通过集成OpenAI Codex来提供智能支持。技术特点上，该项目使用Python开发，以单个Codex技能的形式打包了整个ARS（Academic Research Skills）工作流内容，便于用户安装和更新。适合需要提高科研效率、优化写作及评审过程的研究人员或团队使用，在处理复杂学术任务时尤其能发挥优势。",2,"2026-06-11 03:54:25","CREATED_QUERY"]