HenriquesLab Homebrew Formulas

A Homebrew tap for custom formulas maintained by HenriquesLab.

Installation

Quick Installation (Recommended)

Install formulas directly with a single command:

# Install TaskRepo
brew install henriqueslab/formulas/taskrepo

# Install rxiv-maker
brew install henriqueslab/formulas/rxiv-maker

# Install folder2md4llms
brew install henriqueslab/formulas/folder2md4llms

Alternative: Manual Tap

# Tap this repository first
brew tap henriqueslab/formulas

# Then install formulas
brew install taskrepo
brew install rxiv-maker
brew install folder2md4llms

Available Formulas

📄 Rxiv-Maker

Create beautiful LaTeX manuscripts for preprint servers (bioRxiv, arXiv) with automated formatting and validation.

Installation:

brew install henriqueslab/formulas/rxiv-maker

Quick Start:

rxiv init my-paper          # Create new manuscript
rxiv pdf                    # Generate PDF
rxiv check-installation     # Verify setup

Documentation: https://rxiv-maker.henriqueslab.org Repository: https://github.com/HenriquesLab/rxiv-maker License: MIT

Key Features:

• Automated LaTeX manuscript generation for bioRxiv/arXiv
• Template-based workflow with validation
• Track changes support with latexdiff
• GitHub integration for collaborative writing
• PDF generation with quality checks
• Bibliography management

Dependencies: Python 3.13, LaTeX (TeX Live), git, gh, poppler, latexdiff (all installed automatically)

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📄 folder2md4llms

Convert folder structures and file contents into markdown for Large Language Models.

Installation:

brew install henriqueslab/formulas/folder2md4llms

Quick Start:

folder2md .                     # Process current directory
folder2md /path --limit 80000t  # Process with token limit
folder2md --init-ignore         # Generate ignore file

Documentation: https://folder2md4llms.henriqueslab.org Repository: https://github.com/henriqueslab/folder2md4llms License: MIT

Key Features:

• Smart content condensing for LLMs with token/character limits
• Document conversion (PDF, DOCX, XLSX, PPTX, etc.)
• Binary file analysis
• Parallel processing for large codebases
• Advanced filtering with .gitignore-style patterns
• Interactive file analysis and ignore suggestions
• YAML configuration support

Dependencies: Python 3.13, libmagic (all installed automatically)

Note: Package name is folder2md4llms, command is folder2md.

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📋 TaskRepo

TaskWarrior-inspired task management with markdown files in git repositories.

Installation:

brew install henriqueslab/formulas/taskrepo

Quick Start:

tsk init                  # Initialize configuration
tsk create-repo work      # Create your first repository
tsk add                   # Add a task

Documentation: https://taskrepo.henriqueslab.org Repository: https://github.com/HenriquesLab/TaskRepo License: MIT

Key Features:

• Git-backed task storage with markdown files
• TaskWarrior-inspired workflow (priorities, tags, dependencies, due dates)
• Interactive TUI with autocomplete and color-coded statuses
• Multiple repository support
• GitHub integration for task creation from issues
• Rich YAML frontmatter metadata
• Beautiful terminal output with modern UI

Dependencies: Python 3.13, git, gh (all installed automatically)

Updating Formulas

To update to the latest version of a formula:

brew update
brew upgrade rxiv-maker
brew upgrade folder2md4llms
brew upgrade taskrepo

Uninstalling

# Uninstall a specific formula
brew uninstall rxiv-maker
brew uninstall folder2md4llms
brew uninstall taskrepo

# Untap this repository
brew untap henriqueslab/formulas

Development

Testing formulas locally

# Clone this repository
git clone https://github.com/HenriquesLab/homebrew-formulas.git
cd homebrew-formulas

# Install formula from local file
brew install ./Formula/rxiv-maker.rb
brew install ./Formula/folder2md4llms.rb
brew install ./Formula/taskrepo.rb

Running tests

The repository includes automated tests via GitHub Actions that run on macOS 13 and 14.

To test manually:

# Test installation
brew install formula-name

# Verify executables
rxiv --version
folder2md --version
taskrepo --version
tsk --version

Contributing

Contributions are welcome! Please feel free to submit issues or pull requests.

License

See individual formula files for license information.

Links

• HenriquesLab: https://github.com/HenriquesLab
• rxiv-maker: https://github.com/HenriquesLab/rxiv-maker
• folder2md4llms: https://github.com/henriqueslab/folder2md4llms
• TaskRepo: https://github.com/HenriquesLab/TaskRepo