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brain-guides

https://github.com/flavioguzman/brain-guides

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.2%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: flavioguzman
  • Language: Python
  • Default Branch: master
  • Size: 6.37 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Citation

README.md

Brain Guides Document Processing System

This repository contains a collection of scripts for processing and formatting markdown documents, specifically designed for Brain Guides documentation. The system handles document concatenation, citation formatting, and image processing.

Core Components

Python Scripts

  • markdown_converter.py: The main conversion script that processes markdown files into various output formats (primarily HTML). It integrates with Pandoc and applies various Lua filters during the conversion process.

  • concatenate_markdown.py: Combines multiple markdown files within drug-specific folders into single consolidated documents. It:

    • Preserves YAML front matter from the first file
    • Orders sections based on the order field in YAML
    • Automatically adds a References section
    • Names output files based on the code field from YAML

Lua Filters

  • remove-captions.lua: Removes captions, titles, and alt text from images and figures when remove_captions is set to true in the configuration.

  • image-size.lua: Sets a consistent width (80%) for all images in the document for better visual presentation.

  • reference-list.lua: Formats the references section with custom styling for better readability and mobile responsiveness.

  • citation-spacing.lua: Ensures proper spacing around citations in the text.

Configuration

The system is configured through config.json, which specifies: - Bibliography file path - Citation Style Language (CSL) file path - Default output format - Input file path - Caption removal preferences

Workflow

  1. Source markdown files are organized in drug-specific folders
  2. concatenate_markdown.py combines related files into a single document
  3. markdown_converter.py processes the consolidated file through Pandoc
  4. Lua filters are applied during conversion to handle:
    • Image formatting
    • Citation styling
    • Reference list formatting
    • Caption management

Dependencies

  • Python 3.x
  • Pandoc
  • PyYAML (for markdown concatenation)

Owner

  • Login: flavioguzman
  • Kind: user

Citation (citation-spacing.lua) 

function Cite(cite)
    return {pandoc.Space(), cite}
end

GitHub Events

Total
  • Member event: 2
  • Push event: 8
  • Create event: 2
Last Year
  • Member event: 2
  • Push event: 8
  • Create event: 2

Dependencies

03-interlinking/requirements.txt pypi
  • pyyaml >=6.0.1