Change: Co-expression Network plot: hide the dots if no edge connecte… #18
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| # 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'\W+', '-', title.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) | |
| # 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; | |
| } | |
| nav { | |
| width: 250px; | |
| padding: 20px; | |
| background-color: #2c3e50; | |
| border-right: 1px solid #dee2e6; | |
| position: fixed; | |
| height: 100%; | |
| overflow-y: auto; | |
| } | |
| nav h2 { | |
| color: #ecf0f1; | |
| } | |
| nav a { | |
| display: block; | |
| padding: 8px 16px; | |
| color: #ecf0f1; | |
| text-decoration: none; | |
| } | |
| nav a.active { | |
| background-color: #34495e; | |
| color: #ffffff; | |
| } | |
| nav a:hover { | |
| background-color: #34495e; | |
| color: #ffffff; | |
| } | |
| main { | |
| flex: 1; | |
| padding: 20px; | |
| margin-left: 250px; | |
| overflow-y: auto; | |
| } | |
| h1, h2, h3, h4, h5, h6 { | |
| color: #2c3e50; | |
| } | |
| table { | |
| width: 100%; | |
| margin-bottom: 1rem; | |
| color: #212529; | |
| border-collapse: collapse; | |
| } | |
| table th, | |
| table td { | |
| padding: 0.75rem; | |
| vertical-align: top; | |
| border-top: 1px solid #dee2e6; | |
| } | |
| table thead th { | |
| vertical-align: bottom; | |
| border-bottom: 2px solid #dee2e6; | |
| } | |
| table tbody + tbody { | |
| border-top: 2px solid #dee2e6; | |
| } | |
| .table-responsive { | |
| display: block; | |
| width: 100%; | |
| overflow-x: auto; | |
| -webkit-overflow-scrolling: touch; | |
| } | |
| </style> | |
| </head> | |
| <body> | |
| <nav> | |
| <h2>MetaX</h2> | |
| <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" href="#{{ anchor }}" id="nav-{{ anchor }}">{{ title }}</a> | |
| </li> | |
| {% endfor %} | |
| </ul> | |
| </nav> | |
| <main> | |
| {{ content }} | |
| </main> | |
| <script src="https://code.jquery.com/jquery-3.5.1.slim.min.js"></script> | |
| <script src="https://cdn.jsdelivr.net/npm/@popperjs/core@2.9.2/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'); | |
| // Scroll the navigation to the active link | |
| activeLink.scrollIntoView({ behavior: 'smooth', block: 'center' }); | |
| } | |
| } | |
| }); | |
| } | |
| 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 |