PhDSkills

Codex skills for PhD workflows: writing, publishing, literature handling, research operations, and academic productivity.

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Why This Repository

PhDSkills is a curated skill library for Codex users working in research-heavy environments. It is designed for PhD students, supervisors, research assistants, and academic teams who want reusable, automation-friendly workflows instead of ad hoc prompts.

The repository is structured to scale from a small personal toolbox into a long-lived skills collection covering the full academic lifecycle.

What It Provides

• Writing workflows for academic markdown, manuscripts, thesis drafts, proposals, reports, and revision cycles
• Publishing workflows for DOCX, PDF, HTML, Quarto, Pandoc, templates, references, and validation
• Research operations for reproducible routines, environment checks, project setup, and task automation
• Knowledge workflows for citations, bibliographies, source organization, note pipelines, and reading support
• Future-ready structure for adding many more domain-specific skills without changing the repository conventions

Repository Structure

PhDSkills/
├─ AGENTS.md
├─ README.md
├─ README.zh-CN.md
├─ .gitignore
├─ ai-research-landscape/
│  ├─ SKILL.md
│  ├─ scripts/
│  ├─ assets/
│  ├─ references/
│  └─ agents/
├─ draft-ai-phd-reports/
│  ├─ SKILL.md
│  ├─ scripts/
│  ├─ assets/
│  ├─ references/
│  └─ agents/
├─ frontend-slides/
│  ├─ SKILL.md
│  ├─ scripts/
│  ├─ assets/
│  ├─ references/
│  └─ agents/
├─ md2all/
│  ├─ SKILL.md
│  ├─ scripts/
│  ├─ assets/
│  ├─ references/
│  └─ agents/
├─ agent-project-system/
│  ├─ SKILL.md
│  ├─ scripts/
│  ├─ assets/
│  ├─ references/
│  └─ agents/
├─ report-image-integrator/
│  ├─ SKILL.md
│  ├─ scripts/
│  ├─ assets/
│  ├─ references/
│  └─ agents/
├─ report-to-flowchart-prompt/
│  ├─ SKILL.md
│  ├─ scripts/
│  ├─ assets/
│  ├─ references/
│  └─ agents/
├─ report-to-talk-slides/
│  ├─ SKILL.md
│  ├─ scripts/
│  ├─ assets/
│  ├─ references/
│  └─ agents/
└─ <future-skill>/
   ├─ SKILL.md
   ├─ scripts/
   ├─ assets/
   ├─ references/
   └─ agents/

Skill Catalog

This section is intentionally designed to grow.

Skill	Status	Focus
ai-research-landscape	Available	Verified AI literature landscapes and curated bibliographies
agent-project-system	Available	AI-first project state documents, recovery contracts, and evidence-grounded autonomous progress
draft-ai-phd-reports	Available	AI PhD report drafting, rewriting, and citation-aware polishing
frontend-slides	Available	HTML slide creation and PPT-to-web presentation workflows
md2all	Available	Markdown and Quarto publishing workflows
report-image-integrator	Available	Content-aware figure selection, insertion, renaming, and cross-referencing for Markdown reports
report-to-flowchart-prompt	Available	Flowchart-oriented image prompt generation from reports, proposals, and research plans
report-to-talk-slides	Available	Slide blueprint generation from reports and technical writeups
future-skill	Reserved	Add new skills here as the library expands

Design Principles

• Deterministic first: prefer scripts, assets, and explicit workflows over fuzzy behavior
• Conservative by default: avoid unnecessary rewriting or hidden changes
• Composable: each skill should be usable independently and alongside other skills
• Portable: workflows should remain practical across machines and environments
• Maintainable: repository metadata and documentation must stay synchronized with the actual skill inventory

Adding New Skills

Each skill should live in its own top-level directory and include a SKILL.md as the entrypoint.

Recommended layout:

new-skill/
├─ SKILL.md
├─ scripts/
├─ assets/
├─ references/
└─ agents/

When a new skill is added:

1. Create the skill directory and SKILL.md.
2. Add or update supporting scripts, assets, references, and agents folders as needed.
3. Update the Skill Catalog section in README.md.
4. Update the mirrored catalog in README.zh-CN.md.
5. Keep repository rules in AGENTS.md aligned with the change.

Intended Use Cases

• building a durable personal Codex skill library for doctoral work
• sharing reusable academic workflows across a lab or research group
• standardizing document conversion and publishing routines
• organizing future skills for thesis, papers, reviews, data work, and academic admin

Contributing

Contributions should preserve the repository conventions in AGENTS.md. If you add a new skill, documentation sync is not optional.

Roadmap

• expand beyond publishing into broader PhD research workflows
• introduce more reusable templates and domain-specific utilities
• improve skill discoverability, validation, and onboarding

License

Add a license that matches your intended sharing model before wider distribution.