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Merge branch 'dev' #60

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Merge branch 'dev'

Merge branch 'dev' #60

Workflow file for this run

.github/workflows/jekyll-gh-pages.yml at 5518141
# Sample workflow for building and deploying a Jekyll site to GitHub Pages
name: Deploy Jekyll with GitHub Pages dependencies preinstalled
on:
# Runs on pushes targeting the default branch
push:
branches: ["main"]
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
contents: read
pages: write
id-token: write
# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
concurrency:
group: "pages"
cancel-in-progress: false
jobs:
# Build job
build:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.x'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install markdown jinja2
- name: Convert Markdown to HTML
run: |
python <<EOF
import markdown
from jinja2 import Template
import re
# Read markdown file
markdown_file_path = './Docs/MetaX_Cookbook.md'
with open(markdown_file_path, 'r', encoding='utf-8') as file:
markdown_content = file.read()
# Remove # Contents and [TOC]
markdown_content = markdown_content.replace('# Contents', '').replace('[TOC]', '')
# Extract headings and generate table of contents
headings = re.findall(r'^(#+) (.+)', markdown_content, re.MULTILINE)
toc_items = []
for heading in headings:
level = len(heading[0])
title = heading[1]
anchor = re.sub(r'[^a-zA-Z0-9]+', '-', title.strip()).lower().strip('-')
toc_items.append((level, title, anchor))
# Convert markdown to HTML
html_content = markdown.markdown(markdown_content, extensions=['tables', 'toc'])
# Add Bootstrap classes to tables and images
html_content = re.sub(r'<img (.*?)>', r'<div style="text-align: center;"><img \1 class="img-fluid" style="max-width: 60%; min-width: 300px; height: auto; display: inline-block;"></div>', html_content)
html_content = re.sub(r'<table>', r'<div class="table-responsive"><table class="table table-striped table-bordered">', html_content)
html_content = re.sub(r'</table>', r'</table></div>', html_content)
html_content = re.sub(
r'href="##([^"]+)"', # 匹配类似 ##Module-4.-Peptide-Annotator 的链接
lambda match: f'href="#{re.sub(r"[^a-zA-Z0-9]+", "-", match.group(1).strip()).lower().strip("-")}"',
html_content
)
# Jinja2 template for HTML output
template = Template('''
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>MetaX</title>
<link href="https://stackpath.bootstrapcdn.com/bootswatch/4.5.2/flatly/bootstrap.min.css" rel="stylesheet">
<style>
body {
display: flex;
font-family: Arial, sans-serif;
background-color: #f8f9fa;
margin: 0;
}
nav {
width: 300px;
padding: 20px;
background: linear-gradient(180deg, #34495e, #2c3e50);
border-right: 1px solid #dee2e6;
position: fixed;
height: 100%;
overflow-y: auto;
}
nav h2 {
color: #ecf0f1;
}
nav a {
display: block;
padding: 4px 16px;
color: #ecf0f1;
text-decoration: none;
line-height: 1.2;
margin: 0;
font-size: 0.85rem;
transition: all 0.3s ease-in-out;
}
nav a.level-1 {
font-weight: bold; /* 一级标题加粗 */
font-size: 1rem;
}
nav a.active {
background-color: #0C9277FF;
color: #ffffff;
font-weight: bold;
border-left: 4px solid #0D7A64FF;
}
nav a:hover {
transform: scale(1.05);
background-color: #34495e;
color: #ffffff;
}
main {
flex: 1;
padding: 40px;
margin-left: 300px;
overflow-y: auto;
line-height: 1.6;
}
h1 {
border-bottom: 2px solid #0B8B71FF;
padding-bottom: 10px;
}
h2 {
color: #16a085;
}
h3 {
color: #2980b9;
}
table {
width: 100%;
margin-bottom: 1rem;
color: #212529;
border-collapse: collapse;
box-shadow: 0px 4px 10px rgba(0, 0, 0, 0.1);
border-radius: 8px;
}
table th, table td {
padding: 0.75rem;
vertical-align: top;
border-top: 1px solid #dee2e6;
}
img {
border: 1px solid #ddd;
box-shadow: 2px 2px 10px rgba(0, 0, 0, 0.1);
border-radius: 5px;
}
.table-responsive {
display: block;
width: 100%;
overflow-x: auto;
-webkit-overflow-scrolling: touch;
}
#backToTop {
position: fixed;
bottom: 20px;
right: 20px;
display: none;
background-color: #34495e;
color: #ffffff;
border: none;
padding: 10px 15px;
border-radius: 5px;
cursor: pointer;
transition: background-color 0.3s;
}
#backToTop:hover {
background-color: #0B705CFF;
}
.dark-mode {
background-color: #2c3e50;
color: #ecf0f1;
}
.dark-mode nav {
background-color: #1c2833;
}
.dark-mode nav a {
color: #ecf0f1;
}
</style>
</head>
<body>
<nav>
<h2>MetaX</h2>
<button id="toggleTheme" style="background-color: #ecf0f1; color: #34495e; border: none; padding: 10px; margin-bottom: 10px; cursor: pointer;">Toggle Theme</button>
<ul class="nav flex-column">
{% for level, title, anchor in toc_items %}
<li class="nav-item" style="margin-left: {{ (level - 1) * 20 }}px;">
<a class="nav-link level-{{ level }}" href="#{{ anchor }}" id="nav-{{ anchor }}">{{ title }}</a>
</li>
{% endfor %}
</ul>
</nav>
<main>
{{ content }}
</main>
<button id="backToTop">Top</button>
<script src="https://code.jquery.com/jquery-3.5.1.slim.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/@popperjs/[email protected]/dist/umd/popper.min.js"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js"></script>
<script>
// Function to get the current scroll position and update the active nav link
function updateActiveNavLink() {
var sections = document.querySelectorAll('main h1, main h2, main h3, main h4, main h5, main h6');
var navLinks = document.querySelectorAll('nav a');
var fromTop = window.scrollY + 20;
sections.forEach(function(section) {
var top = section.offsetTop;
var bottom = top + section.offsetHeight;
var id = section.id;
if (fromTop >= top && fromTop < bottom) {
navLinks.forEach(function(link) {
link.classList.remove('active');
});
var activeLink = document.querySelector('nav a[href="#' + id + '"]');
if (activeLink) {
activeLink.classList.add('active');
activeLink.scrollIntoView({ behavior: 'smooth', block: 'center' });
}
}
});
}
// Show/hide back-to-top button
window.addEventListener('scroll', function () {
var backToTop = document.getElementById('backToTop');
if (window.scrollY > 300) {
backToTop.style.display = 'block';
} else {
backToTop.style.display = 'none';
}
});
// Scroll to top
document.getElementById('backToTop').addEventListener('click', function () {
window.scrollTo({ top: 0, behavior: 'smooth' });
});
// Toggle theme
document.getElementById('toggleTheme').addEventListener('click', function () {
document.body.classList.toggle('dark-mode');
});
window.addEventListener('scroll', updateActiveNavLink);
</script>
</body>
</html>
''')
# Render the template with the content and TOC items
html_output = template.render(content=html_content, toc_items=toc_items)
# Write the HTML output to a file
output_file_path = './Docs/index.html'
with open(output_file_path, 'w', encoding='utf-8') as file:
file.write(html_output)
print("HTML file has been generated successfully.")
EOF
- name: Setup Pages
uses: actions/configure-pages@v5
- name: Build with Jekyll
uses: actions/jekyll-build-pages@v1
with:
source: ./Docs/
destination: ./_site
- name: Upload artifact
uses: actions/upload-pages-artifact@v3
# Deployment job
deploy:
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}
runs-on: ubuntu-latest
needs: build
steps:
- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v4