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Agent skill

Research Publishing

by fcakyon in fcakyon/phd-skills

A skill your agent uses when the user wants to prepare code for open-source release, create reproducible research artifacts, or structure a repository for publication.

MITAuto-check passedResearch & Science

Install Research Publishing

skills CLI
$ npx skills add fcakyon/phd-skills --skill research-publishing -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install fcakyon/phd-skills research-publishing --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/fcakyon/phd-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/plugin/skills/research-publishing .claude/skills/research-publishing && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
research-publishing
GitHub stars
414
Token cost
~1.1k tokens
SKILL.md length
441 words
Files
1
Skills in repo
12
Repo updated
First seen
Licence
MIT

At a glance

A skill your agent uses when the user wants to prepare code for open-source release, create reproducible research artifacts, or structure a repository for publication.

  • Works in 7 steps: Repository Assessment → Repository Structure → Reproducibility Checklist → …
  • The user wants to prepare code for open-source release
  • SKILL.md covers Step 1: Repository Assessment, Step 2: Repository Structure, Step 3: Reproducibility… and Step 4: README Structure, plus 4 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Research Publishing is an agent skill from fcakyon/phd-skills. Use when the user wants to prepare code for open-source release, create reproducible research artifacts, or structure a repository for publication. Triggers on phrases like "publish code", "open source release", "reproducibility", "research repository", "code release", or "prepare for publication".

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Reproducible research. The repository describes itself as: PhD Research Skills for Claude Code: paper reproduction, experiment design, paper review, result comparison and more. The licence is MIT.

When your agent uses it

  • The user wants to prepare code for open-source release
  • Create reproducible research artifacts
  • Structure a repository for publication
  • Phrases like publish code

Example prompts

  • “publish code”
  • “open source release”
  • “reproducibility”
  • “/research-publishing”

Workflow steps

7 steps, taken from the step headings in SKILL.md.

  1. Repository Assessment
  2. Repository Structure
  3. Reproducibility Checklist
  4. README Structure
  5. Code Cleanup
  6. License Selection
  7. Pre-Release Testing

What it can do on your machine

Read from SKILL.md and the folder at commit 67acd61. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Research Publishing loads about 1.1k tokens when it runs. Until then it costs about 80 tokens; SKILL.md has 441 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~80
When it runs · the whole SKILL.md, loaded when a task matches
~1.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from fcakyon/phd-skills at commit 67acd61, republished under its MIT licence (© fcakyon). 441 words, ~1,095 tokens.

Download SKILL.mdSave it as .claude/skills/research-publishing/SKILL.md (or your agent's skills folder).
name
research-publishing
description
Use when the user wants to prepare code for open-source release, create reproducible research artifacts, or structure a repository for publication. Triggers on phrases like "publish code", "open source release", "reproducibility", "research repository", "code release", or "prepare for publication".

Research Publishing Methodology

You are helping a researcher prepare their code and artifacts for public release alongside a paper submission.

Step 1: Repository Assessment

Before any changes, audit the current state:

  1. Sensitive content scan:

    • API keys, tokens, credentials (grep for common patterns)
    • Hardcoded paths specific to the researcher's machine
    • Internal URLs or private infrastructure references
    • Personal identifiable information in comments or data

  2. Dependency audit:

    • List all dependencies with pinned versions
    • Identify any proprietary or restricted-license dependencies
    • Check for abandoned/unmaintained dependencies
    • Verify all dependencies are pip/conda installable

  3. Code organization:

    • Identify dead code, debugging artifacts, scratch files
    • Find duplicated code that should be unified
    • Check for overly complex code that can be simplified

Step 2: Repository Structure

A publishable research repository should have:

project/
  README.md            # Installation, usage, citation
  LICENSE              # Must have an explicit license
  requirements.txt     # or pyproject.toml with pinned deps
  setup.py / setup.cfg # Package installation
  src/                 # Source code
  scripts/             # Training, evaluation, inference scripts
  configs/             # Configuration files
  data/                # Sample data or download instructions
  checkpoints/         # Download instructions (not actual weights)
  results/             # Key result files referenced in paper

Step 3: Reproducibility Checklist

For each experiment in the paper:

  • Configuration file exists and matches paper's hyperparameters
  • Random seeds are set and documented
  • Training command is documented end-to-end
  • Evaluation command produces the reported numbers
  • Data preprocessing steps are scripted (not manual)
  • Hardware requirements are documented (GPU type, memory, time)
  • Dependencies are version-pinned

Step 4: README Structure

A research README must include:

  1. Title + one-line description
  2. Paper link (arXiv, venue page)
  3. Visual (architecture diagram, key result figure, or demo GIF)
  4. Installation (step-by-step, tested on clean environment)
  5. Quick start (inference on a single example, < 5 commands)
  6. Training (full reproduction commands)
  7. Evaluation (reproduce paper numbers)
  8. Model zoo / checkpoints (download links with expected metrics)
  9. Citation (BibTeX block)
  10. License
Show full SKILL.md (194 more words)Show less

Step 5: Code Cleanup

Apply minimal, targeted cleanup:

  1. Remove debugging prints, commented-out code, scratch experiments
  2. Replace hardcoded paths with configurable paths (env vars or args)
  3. Add docstrings to public functions (not internal helpers)
  4. Ensure the main entry points are clearly documented
  5. Do NOT refactor working code for style — it adds risk for no benefit

Step 6: License Selection

Guide the user through license choice:

LicenseAllows commercial useRequires attributionCopyleft
MITYesYesNo
Apache 2.0YesYesNo (patent grant)
GPL 3.0YesYesYes (derivative works)
CC BY 4.0YesYesNo (for non-code)
CC BY-NC 4.0NoYesNo (for non-code)

Default recommendation: MIT for code, CC BY 4.0 for datasets/models.

Step 7: Pre-Release Testing

Before publishing:

  1. Clone into a fresh directory
  2. Follow README installation steps exactly
  3. Run quick start commands
  4. Run evaluation to verify numbers match paper
  5. Check that no sensitive information is in git history

Output Format

Produce:

  1. Audit report: sensitive content found, dependency issues, dead code
  2. Action list: specific files to modify/remove/add
  3. README draft: following the structure above
  4. Reproducibility checklist: per-experiment verification status

© fcakyon, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in plugin/skills/research-publishing of fcakyon/phd-skills.

Open the folder on GitHubat commit 67acd61

Compare with similar skills

Research Publishing next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Research Publishing compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Research Publishing this skillfcakyon/phd-skills414—~1.1kAutomated safety check: PassMIT
Peer ReviewK-Dense-AI/claude-scientific-writer2.4k2 repos~3.1kAutomated safety check: NotesMIT
Compute Environment Setupaipoch/open-science5.5k1 repos~2.6kAutomated safety check: PassApache-2.0
CHARLS Paper Reproduction Guidexjtulyc/MedgeClaw6171 repos~1.8kAutomated safety check: PassNone
Figure Styleaipoch/open-science5.5k—~5.1kAutomated safety check: PassApache-2.0
Add Bactopia Toolbactopia/bactopia522—~4.1kAutomated safety check: PassMIT

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Categories

Questions about Research Publishing

What does Research Publishing do?

A skill your agent uses when the user wants to prepare code for open-source release, create reproducible research artifacts, or structure a repository for publication. Research Publishing is an agent skill from fcakyon/phd-skills. Use when the user wants to prepare code for open-source release, create reproducible research artifacts, or structure a repository for publication.

When should I use Research Publishing?

Research Publishing fits situations like: the user wants to prepare code for open-source release; create reproducible research artifacts; structure a repository for publication; phrases like publish code.

How do I install Research Publishing in Claude Code?

Run `npx skills add fcakyon/phd-skills --skill research-publishing -a claude-code`. Or copy the skill folder (plugin/skills/research-publishing in fcakyon/phd-skills) into .claude/skills/research-publishing in your project. Claude Code loads it when a task matches its description.

How do I install Research Publishing in Codex?

Run `npx skills add fcakyon/phd-skills --skill research-publishing -a codex`. Or copy the skill folder (plugin/skills/research-publishing in fcakyon/phd-skills) into .agents/skills/research-publishing in your project. Codex loads it when a task matches its description.

Can I use Research Publishing in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add fcakyon/phd-skills --skill research-publishing -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/research-publishing, .gemini/skills/research-publishing, .github/skills/research-publishing and .opencode/skills/research-publishing in your project.

What does Research Publishing need to run?

SKILL.md names no scripts, command-line tools or credentials: Research Publishing is instructions for the agent only.

Does Research Publishing access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Research Publishing safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Research Publishing use?

Research Publishing is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Research Publishing use?

About 1.1k tokens (SKILL.md is roughly 4.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Research Publishing?

Skills that share tags, products or a category with Research Publishing: Peer Review (K-Dense-AI/claude-scientific-writer, 2.4k stars), Compute Environment Setup (aipoch/open-science, 5.5k stars), CHARLS Paper Reproduction Guide (xjtulyc/MedgeClaw, 617 stars) and Figure Style (aipoch/open-science, 5.5k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Research Publishing?

fcakyon (a GitHub user) maintains it in fcakyon/phd-skills, which has 414 GitHub stars. The repository holds 12 skills in this directory. The repository was last updated on September 16, 2026.

Source: fcakyon/phd-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.