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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Overview

Hugo personal website for Badran Elshenawy (bioinformatician, Oxford postdoc). Uses the Coder theme, deployed on Netlify. Contains 85+ blog posts across multiple tutorial series.

Development Commands

hugo server -D    # Local dev server with drafts
hugo server       # Local dev server without drafts
hugo              # Production build (output to public/)

Architecture

  • Config: hugo.toml (site metadata, theme, social links, nav, taxonomies)
  • Deploy: netlify.toml (Hugo v0.141.0)
  • Theme: themes/Coder/ (git submodule — do not edit directly)
  • Archetype: archetypes/default.md (uses +++ TOML front matter, but actual posts use --- YAML)

Content Conventions

Dual-file pattern

Every blog post exists as two files: a .rmd source and a rendered .md file. Both are committed. The .rmd is the source of truth; the .md is generated via hugodown::md_document.

Post naming

Files use {series_name}_part_{N}.md format with underscores:

  • scrna_seq_series_part_15.md
  • claude_series_part_8.md
  • bulk_RNA_Seq_part_10.md
  • tidyverse_series_part_14.md
  • Standalone posts: my_first_post.md, vs_code_quarto_visual_mode.md

Front matter (YAML with --- delimiters)

Required fields for blog posts:

title: "Series Name – Post N: Subtitle"
author: "Badran Elshenawy"
date: 2026-01-01T08:00:00Z
categories: [...]
tags: [...]
description: "..."
slug: "url-friendly-slug"
draft: false
output: hugodown::md_document
summary: "..."
rmd_hash: <hash>

Optional: aliases, featured

Taxonomies

Four taxonomy types are configured: categories, series, tags, authors.

Images

  • Post-specific images: content/posts/images/
  • Site-wide images (avatar, etc.): static/images/

Hugo config notes

  • markup.goldmark.renderer.unsafe = true — raw HTML is allowed in markdown (needed for Rmd rendering)
  • Pagination: 6 posts per page
  • Color scheme: auto with toggle enabled

Commit Message Convention

Lowercase, descriptive format: {series} post {N}: {topic} Examples: claude series post 8: subagents, scRNA-Seq series post 15: pea theory

Deployment

Auto-deploys to Netlify on push to main. Live at: https://badran-elshenawy.netlify.app/