How to Reference Files from GitHub

This guide shows you different ways to reference and link to files in your GitHub repositories.

Your GitHub Profile

Based on your profile at https://github.com/bio-info, you have several repositories that you can reference:

• advanced-bioreactor - Arduino code for pH, temperature monitoring
• air-quality-analysis - Python code for PM2.5 analysis
• weatherstation - ESP8266 weather monitoring
• arduinos - Arduino code collection

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Method 1: Direct Links to Files

Link to a Specific File

[View the Arduino code](https://github.com/bio-info/advanced-bioreactor/blob/main/bioreactor.ino)

Example: View the Arduino code

Link to a Specific Line in a File

[View line 42](https://github.com/bio-info/advanced-bioreactor/blob/main/bioreactor.ino#L42)

Link to a Range of Lines

[View lines 10-20](https://github.com/bio-info/advanced-bioreactor/blob/main/bioreactor.ino#L10-L20)

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Method 2: Embed Code from GitHub

Display Code Snippet

You can copy code from your GitHub repos and display it here:

# From air-quality-analysis repository
import pandas as pd
import matplotlib.pyplot as plt

def analyze_pm25(data):
    """Analyze PM2.5 data from sensors"""
    df = pd.DataFrame(data)
    return df['pm25'].describe()

With Attribution

# Source: https://github.com/bio-info/air-quality-analysis
# File: analysis/pm25_analysis.py

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Method 3: GitHub Raw File URLs

For direct file access (CSV, JSON, images), use raw URLs:

Data Files

Download the data: [PM25_data.csv](https://raw.githubusercontent.com/bio-info/air-quality-analysis/main/data/PM25_data.csv)

Images

![Sensor Setup](https://raw.githubusercontent.com/bio-info/weatherstation/main/images/setup.jpg)

JSON Configuration

[Download config.json](https://raw.githubusercontent.com/bio-info/arduinos/main/config.json)

Format:

https://raw.githubusercontent.com/USERNAME/REPOSITORY/BRANCH/path/to/file

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Method 4: GitHub Gist Embeds

If you create GitHub Gists, you can embed them:

<script src="https://gist.github.com/bio-info/GIST_ID.js"></script>

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Method 5: Reference Repository Files Locally

You can download files from your GitHub repos and include them in this Jekyll site:

Step 1: Add files to your Jekyll site

# Create a downloads folder
mkdir -p assets/downloads

# Add files from your repos
cp ~/path/to/file.csv assets/downloads/

Step 2: Reference them in your documentation

Download: [PM2.5 Dataset](/assets/downloads/pm25_data.csv)

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Method 6: Link to GitHub Pages from Other Repos

If your other repositories have GitHub Pages enabled:

View the live demo: [Weather Station Dashboard](https://bio-info.github.io/weatherstation)

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Method 7: Submodules (Advanced)

You can include entire repositories as submodules:

# Add a submodule
git submodule add https://github.com/bio-info/air-quality-analysis code/air-quality

# Reference files
[Analysis Code](code/air-quality/analysis.py)

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Example: Creating a Project Showcase Page

Here’s how to create a page showcasing your projects:

---
layout: default
title: My Projects
---

# Research Projects

## Air Quality Analysis
Analyzing PM2.5 data using Python and machine learning.

- **Repository:** [air-quality-analysis](https://github.com/bio-info/air-quality-analysis)
- **Technologies:** Python, Pandas, Jupyter
- **View Code:** [Main Analysis Script](https://github.com/bio-info/air-quality-analysis/blob/main/analysis.py)
- **Data:** [Download Sample Data](https://raw.githubusercontent.com/bio-info/air-quality-analysis/main/data/sample.csv)

## Advanced Bioreactor
Arduino-based monitoring system for algae bioreactors.

- **Repository:** [advanced-bioreactor](https://github.com/bio-info/advanced-bioreactor)
- **Technologies:** Arduino, C++, Python
- **Documentation:** [Setup Guide](https://github.com/bio-info/advanced-bioreactor#readme)

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Best Practices

1. Use Relative Links within this site:

   [See Getting Started](/docs/getting-started.html)
   

2. Use Absolute GitHub URLs for external repos:

   [View Source](https://github.com/bio-info/REPO/blob/main/file.py)
   

3. Keep URLs Updated: If you rename branches or files, update links

4. Use Raw URLs for Downloads: For CSV, JSON, images that users will download

5. Add Context: Always explain what the link is:

   ❌ [Click here](https://github.com/...)
   ✅ [View the Arduino sensor code](https://github.com/...)
   

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Your Configured GitHub Integration

This site is already configured to work with your GitHub account:

• Profile: https://github.com/bio-info
• “View on GitHub” button links to your profile (top right)
• “Edit this page” buttons will link to files in your repository
• Repository URL: Will be set when you create the repo

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Next Steps

1. Create Your Repository

   # On GitHub, create a new repo named: bio-info.github.io
   

2. Push Your Jekyll Site

   cd /Users/binh.nguyen2/working/jeky
   git init
   git add .
   git commit -m "Initial Jekyll site"
   git remote add origin https://github.com/bio-info/bio-info.github.io.git
   git push -u origin main
   

3. Enable GitHub Pages
   • Go to repository Settings → Pages
   • Select source: Deploy from branch main
   • Your site will be live at: https://bio-info.github.io
4. Reference Your Other Repos
   • Create pages linking to your existing projects
   • Embed code examples from your repositories
   • Link to datasets and resources

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Quick Reference Table

What to Link	URL Format	Example
File in repo	https://github.com/USER/REPO/blob/BRANCH/path	Link
Raw file	https://raw.githubusercontent.com/USER/REPO/BRANCH/path	Link
Specific line	Add #L42 to file URL	Link
Line range	Add #L10-L20 to file URL	Link
Repository	https://github.com/USER/REPO	Link
Your profile	https://github.com/USER	Link