diff --git a/.gitignore b/.gitignore index fb2762de..6a81b208 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,7 @@ pnpm-debug.log* # macOS-specific files .DS_Store + +# Nextflow execution artifacts +src/pages/examples/*/work/ +src/pages/examples/*/.nextflow* diff --git a/astro.config.mjs b/astro.config.mjs index 22355017..5671a456 100644 --- a/astro.config.mjs +++ b/astro.config.mjs @@ -3,7 +3,9 @@ import { defineConfig } from "astro/config"; import remarkDescription from "astro-remark-description"; import remarkDirective from "remark-directive"; import sitemap from "@astrojs/sitemap"; -import { transformerNotationDiff, transformerNotationFocus, transformerMetaHighlight } from "@shikijs/transformers"; +import expressiveCode from "astro-expressive-code"; +import { pluginLineNumbers } from "@expressive-code/plugin-line-numbers"; +import mdx from "@astrojs/mdx"; import react from "@astrojs/react"; import tailwind from "@astrojs/tailwind"; @@ -12,12 +14,6 @@ export default defineConfig({ site: "https://nextflow.io/", outDir: "./output", markdown: { - shikiConfig: { - // Choose from Shiki's built-in themes (or add your own) - // https://shiki.style/themes - theme: "light-plus", - transformers: [transformerNotationDiff(), transformerNotationFocus(), transformerMetaHighlight()], - }, remarkPlugins: [ remarkDirective, admonitionsPlugin, @@ -52,6 +48,8 @@ export default defineConfig({ ], }, integrations: [ + expressiveCode(), + mdx(), react(), tailwind(), sitemap({ diff --git a/ec.config.mjs b/ec.config.mjs new file mode 100644 index 00000000..65f6b2af --- /dev/null +++ b/ec.config.mjs @@ -0,0 +1,85 @@ +import { defineEcConfig } from "astro-expressive-code"; +import { pluginLineNumbers } from "@expressive-code/plugin-line-numbers"; + +export default defineEcConfig({ + // Use light theme for consistency with site design + themes: ["github-light"], + + // Enable advanced features + plugins: [pluginLineNumbers()], + + // Disable Expressive Code's built-in copy button and enable line numbers + defaultProps: { + showCopyToClipboardButton: false, + showLineNumbers: true, + }, + + // Comprehensive styling to match site's clean, minimal design + styleOverrides: { + // Core background and text styling - pure white like site + codeBackground: "#ffffff", + codeForeground: "#24292f", // GitHub light theme text color + + // Typography - match site's exact monospace stack + codeFontFamily: "Menlo, Monaco, Consolas, 'Courier New', monospace", + codeFontSize: "1.25rem", // 20px - readable code size, smaller than before + codeLineHeight: "1.5", + + // Borders - subtle gray matching site's container styling + borderColor: "#e5e7eb", // rgb(229, 231, 235) - light gray + borderWidth: "1px", + borderRadius: "0.375rem", // Tailwind rounded-md + + // Text markers - use site's green color scheme for highlighting + textMarkers: { + // Use the site's actual light green color for highlighting + markBackground: "var(--nextflow-light-green)", // Direct use of site color + markBorderColor: "transparent", // Clean, no borders + + // Make highlighting more visible but still clean + backgroundOpacity: "0.4", // More visible highlighting + borderOpacity: "0", // No border opacity + + // Make text more readable on light green background + markForeground: "#1f2937", // Dark text for better contrast + + // Label styling with bright green background + lineMarkerLabelColor: "#0dc09d", // Bright green for labels + }, + + // Frames - clean, minimal styling + frames: { + // Remove all shadows and heavy styling + shadowColor: "transparent", + frameBoxShadowCssValue: "none", + + // Clean frame styling matching site containers + editorBackground: "#ffffff", + editorActiveTabBackground: "#f9fafb", // Very light gray for active tab + editorActiveTabBorderColor: "#e5e7eb", // Match border color + editorTabBarBackground: "#ffffff", + editorTabBarBorderColor: "#e5e7eb", + + // Terminal-style frame styling + terminalBackground: "#ffffff", + terminalTitlebarBackground: "#f9fafb", + terminalTitlebarForeground: "#6b7280", // Subtle gray text + terminalTitlebarBorderColor: "#e5e7eb", + }, + + // Focus and selection states + focusBorder: "var(--nextflow-green)", // Use site's green for focus + codeSelectionBackground: "var(--nextflow-light-green)", // Use site's light green + + // Scrollbar styling + scrollbarThumbColor: "#d1d5db", // Light gray + scrollbarThumbHoverColor: "#9ca3af", // Slightly darker on hover + + // Ensure clean, minimal appearance throughout + uiSelectionBackground: "var(--nextflow-light-green)", + uiSelectionForeground: "#1f2937", // Dark text for contrast + + // Larger UI text for better readability of frame titles + uiFontSize: "1.2rem", // Increased from default 0.9rem for more prominent titles + }, +}); diff --git a/netlify.toml b/netlify.toml index 1079e020..ca664d86 100644 --- a/netlify.toml +++ b/netlify.toml @@ -23,20 +23,41 @@ [[redirects]] from = "/example1.html" - to = "/basic-pipeline.html" + to = "/examples/basic-pipeline" [[redirects]] from = "/example2.html" - to = "/mixing-scripting-languages.html" + to = "/examples/mixing-scripting-languages" [[redirects]] from = "/example3.html" - to = "/blast-pipeline.html" + to = "/examples/blast-pipeline" [[redirects]] from = "/example4.html" - to = "/rna-seq-pipeline.html" + to = "/examples/rna-seq-pipeline" [[redirects]] from = "/example5.html" - to = "/machine-learning-pipeline.html" \ No newline at end of file + to = "/examples/machine-learning-pipeline" + +# Direct redirects from old .html files to new structure +[[redirects]] + from = "/basic-pipeline.html" + to = "/examples/basic-pipeline" + +[[redirects]] + from = "/mixing-scripting-languages.html" + to = "/examples/mixing-scripting-languages" + +[[redirects]] + from = "/blast-pipeline.html" + to = "/examples/blast-pipeline" + +[[redirects]] + from = "/rna-seq-pipeline.html" + to = "/examples/rna-seq-pipeline" + +[[redirects]] + from = "/machine-learning-pipeline.html" + to = "/examples/machine-learning-pipeline" \ No newline at end of file diff --git a/package-lock.json b/package-lock.json index 70340d99..2bb248b7 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,11 +9,14 @@ "version": "0.0.1", "dependencies": { "@astrojs/check": "^0.9.3", + "@astrojs/mdx": "^3.1.9", "@astrojs/react": "^4.2.1", "@astrojs/rss": "^4.0.7", "@astrojs/sitemap": "^3.1.6", + "@expressive-code/plugin-line-numbers": "^0.41.3", "@shikijs/transformers": "^1.6.3", "astro": "^4.16.1", + "astro-expressive-code": "^0.41.3", "astro-remark-description": "^1.1.2", "react": "^19.0.0", "react-cookie": "^7.2.2", @@ -153,6 +156,34 @@ "vfile": "^6.0.3" } }, + "node_modules/@astrojs/mdx": { + "version": "3.1.9", + "resolved": "https://registry.npmjs.org/@astrojs/mdx/-/mdx-3.1.9.tgz", + "integrity": "sha512-3jPD4Bff6lIA20RQoonnZkRtZ9T3i0HFm6fcDF7BMsKIZ+xBP2KXzQWiuGu62lrVCmU612N+SQVGl5e0fI+zWg==", + "license": "MIT", + "dependencies": { + "@astrojs/markdown-remark": "5.3.0", + 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"sha512-KaFVRjoqLyF6YXCbVLNad/eS4+OfPQQn2yOd7zF/h5T/CSL2v8NpN6a5TPvtbXthAGw5nG+PuTtq+DdIZr+cRQ==", + "license": "MIT", + "dependencies": { + "@types/unist": "^3.0.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/unified" + } + }, "node_modules/unist-util-remove-position": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/unist-util-remove-position/-/unist-util-remove-position-5.0.0.tgz", @@ -7319,7 +8300,6 @@ "version": "1.0.2", "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz", "integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw==", - "dev": true, "license": "MIT" }, "node_modules/vfile": { diff --git a/package.json b/package.json index dd21a83a..51cada0c 100644 --- a/package.json +++ b/package.json @@ -12,11 +12,14 @@ }, "dependencies": { "@astrojs/check": "^0.9.3", + "@astrojs/mdx": "^3.1.9", "@astrojs/react": "^4.2.1", "@astrojs/rss": "^4.0.7", "@astrojs/sitemap": "^3.1.6", + "@expressive-code/plugin-line-numbers": "^0.41.3", "@shikijs/transformers": "^1.6.3", "astro": "^4.16.1", + "astro-expressive-code": "^0.41.3", "astro-remark-description": "^1.1.2", "react": "^19.0.0", "react-cookie": "^7.2.2", diff --git a/src/components/CodeBlock/CodeCopy.tsx b/src/components/CodeBlock/CodeCopy.tsx deleted file mode 100644 index 0dda0a42..00000000 --- a/src/components/CodeBlock/CodeCopy.tsx +++ /dev/null @@ -1,88 +0,0 @@ -import React, { useEffect, useState, useCallback } from 'react'; - -export default function CodeCopyButton() { - const [tooltipVisible, setTooltipVisible] = useState(false); - const [tooltipPosition, setTooltipPosition] = useState<{ x: number, y: number }>({ x: 0, y: 0 }); - - const addCopyButtons = useCallback(() => { - const codeBlocks = document.querySelectorAll('pre > code'); - - codeBlocks.forEach((codeBlock) => { - const parent = codeBlock.parentElement; - if (parent && !parent.querySelector('.copy-button')) { - const button = document.createElement('button'); - button.className = 'copy-button'; - button.title = 'Copy to clipboard'; - button.innerHTML = ` - - Copied! - `; - - parent.style.position = 'relative'; - - button.addEventListener('click', (e) => { - const code = codeBlock.textContent || ''; - - navigator.clipboard.writeText(code).then(() => { - const tooltip = button.querySelector('.copy-tooltip'); - if (tooltip) { - tooltip.classList.add('visible'); - setTimeout(() => { - tooltip.classList.remove('visible'); - }, 2000); - } - }).catch(err => { - console.error('Error al copiar: ', err); - }); - }); - - parent.appendChild(button); - } - }); - }, []); - - const addLinkClassToAnchors = useCallback(() => { - const paragraphs = document.querySelectorAll('.code-examples p, .blg-summary p'); - - paragraphs.forEach((paragraph) => { - const links = paragraph.querySelectorAll('a'); - - links.forEach((link) => { - if (!link.classList.contains('link')) { - link.classList.add('link'); - } - }); - }); - }, []); - - useEffect(() => { - const setupPage = () => { - addCopyButtons(); - addLinkClassToAnchors(); - }; - - setupPage(); - - const observer = new MutationObserver(setupPage); - - observer.observe(document.documentElement, { - childList: true, - subtree: true - }); - - window.addEventListener('load', setupPage); - - return () => { - observer.disconnect(); - window.removeEventListener('load', setupPage); - document.querySelectorAll('.copy-button').forEach((button) => { - button.remove(); - }); - }; - }, [addCopyButtons, addLinkClassToAnchors]); - - return null; -} \ No newline at end of file diff --git a/src/components/CodeBlock/styles.css b/src/components/CodeBlock/styles.css deleted file mode 100644 index 1f67cace..00000000 --- a/src/components/CodeBlock/styles.css +++ /dev/null @@ -1,91 +0,0 @@ -pre { - position: relative; - overflow: visible !important; -} - -.copy-button { - position: absolute; - top: 10px; - right: 10px; - background: rgba(255, 255, 255, 0.1); - border: none; - border-radius: 4px; - color: #6e7781; - padding: 5px; - cursor: pointer; - display: flex; - align-items: center; - justify-content: center; - opacity: 0.7; - transition: opacity 0.2s, background-color 0.2s; -} - -.copy-button:hover { - opacity: 1; - background-color: rgba(255, 255, 255, 0.2); - color: var(--color-brand); -} - -.copy-tooltip { - position: absolute; - top: -30px; - left: 50%; - transform: translateX(-50%); - background-color: #333; - color: white; - padding: 4px 8px; - border-radius: 4px; - font-size: 12px; - opacity: 0; - visibility: hidden; - transition: opacity 0.2s, visibility 0.2s; - white-space: nowrap; - min-width: max-content; - z-index: 1000; - pointer-events: none; -} - -.copy-tooltip.visible { - opacity: 1; - visibility: visible; -} - -.copy-tooltip:after { - content: ""; - position: absolute; - top: 100%; - left: 50%; - margin-left: -5px; - border-width: 5px; - border-style: solid; - border-color: #333 transparent transparent transparent; -} - -.code-examples p a, -.blg-summary p a { - color: #087f68; - text-decoration: none; -} - -.code-examples p a:hover, -.code-examples p a:focus, -.blg-summary p a:hover, -.blg-summary p a:focus { - text-decoration: underline; - color: #087f68; - transition: all 0.3s; -} - -.code-examples p a.link, -.blg-summary p a.link { - color: #087f68; -} - -pre a, code a { - color: inherit !important; - text-decoration: none !important; -} - -pre a:hover, code a:hover { - text-decoration: none !important; -} \ No newline at end of file diff --git a/src/components/Footer.astro b/src/components/Footer.astro index 97449b1e..799a84a5 100644 --- a/src/components/Footer.astro +++ b/src/components/Footer.astro @@ -86,29 +86,30 @@ import LogoSeqera from "../../public/img/assets/Logo_Seqera_whote.svg";