From 0ce0002777511b7d3e89762e900e5b23e1c67599 Mon Sep 17 00:00:00 2001 From: Kevin F Date: Thu, 14 Nov 2024 10:58:48 +0100 Subject: [PATCH 1/2] setup mermaid component --- CONTRIBUTING.md | 86 +- package-lock.json | 1327 +++++++++++++++++++++++++++--- package.json | 1 + src/components/mdx/Mermaid.astro | 67 ++ 4 files changed, 1332 insertions(+), 149 deletions(-) create mode 100644 src/components/mdx/Mermaid.astro diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d77da0955..880db536a 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -14,10 +14,11 @@ Your contribution to the DataPLANT Knowledge Base is highly appreciated. This gu - [Guides](#guides) - [``](#specific-tool) - [Core concepts](#core-concepts) + - [Authors](#authors) - [Style Guide](#style-guide) + - [Composition](#composition) - [Use Starlight components](#use-starlight-components) - - [General file information](#general-file-information) - - [Authors](#authors) + - [Use Custom components](#use-custom-components) - [Images](#images) - [html](#html) - [Tables](#tables) @@ -78,30 +79,6 @@ If you have a tool that is used in the context of an ARC, you can place the docu Basic information about RDM, not necessary ARC related. -## Style Guide - -### Use Starlight components - -The Starlight framework has some nice components that can be used in the `.mdx` files. - -Have an eye on the existing components to improve the readability of the content. - -[Starlight components](https://starlight.astro.build/components/using-components/) - -### General file information - -- All files and folders must always be [kebap-case](https://developer.mozilla.org/en-US/docs/Glossary/Kebab_case). This means all lower case and `-` as word separator. - -```txt title="Example" -src\assets\images\arc-commander\access-2.png -``` - -#### Composition - -Always follow **DRY (Don't Repeat Yourself)** principle. If you have the same content in multiple places, consider creating a reusable component. - -In `.mdx` you can not only link to other content, but also directly insert other content in the current file. - ### Authors Authors listed via a file in [`src/content/authors`](src/content/authors) can easily be mentioned in the yaml header of articles. @@ -128,6 +105,63 @@ authors: - kevin-frey ``` +## Style Guide + + +All files and folders must always be [kebap-case](https://developer.mozilla.org/en-US/docs/Glossary/Kebab_case). This means all lower case and `-` as word separator. + +```txt title="Example" +src\assets\images\arc-commander\access-2.png +``` + +### Composition + +Always follow **DRY (Don't Repeat Yourself)** principle. If you have the same content in multiple places, consider creating a reusable component. + +In `.mdx` you can not only link to other content, but also directly insert other content in the current file. + + +### Use Starlight components + +The Starlight framework has some nice components that can be used in the `.mdx` files. + +Have an eye on the existing components to improve the readability of the content. + +[Starlight components](https://starlight.astro.build/components/using-components/) + +### Use Custom components + +Checkout the `src/components/mdx` directory for custom components. + +#### Mermaid + +Can only be used in mdx files. + +```mdx +import Mermaid from '@components/mdx/Mermaid.astro' + + +```mermaid +flowchart LR + markdown["`This **is** _Markdown_`"] + newLines["`Line1 + Line 2 + Line 3`"] + markdown --> newLines +``` + +``` + +#### Viola Says + +```mdx +import ViolaSays from '@components/ViolaSays.astro' + + +Ok, I think I understand. The study is used to describe the overall experiment and the sample generation. Then the assays are used to describe the individual lab processes and the data generation! + +``` + ### Images #### How to store diff --git a/package-lock.json b/package-lock.json index 8c030e5c5..6b16982ce 100755 --- a/package-lock.json +++ b/package-lock.json @@ -16,6 +16,7 @@ "astro": "^4.15.3", "astro-icon": "^1.1.1", "html-escaper": "^3.0.3", + "mermaid": "^11.4.0", "rehype-autolink-headings": "^7.1.0", "rehype-slug": "^6.0.0", "sharp": "^0.32.5", @@ -634,6 +635,51 @@ "node": ">=6.9.0" } }, + "node_modules/@braintree/sanitize-url": { + "version": "7.1.0", + "resolved": "https://registry.npmjs.org/@braintree/sanitize-url/-/sanitize-url-7.1.0.tgz", + "integrity": "sha512-o+UlMLt49RvtCASlOMW0AkHnabN9wR9rwCCherxO0yG4Npy34GkvrAqdXQvrhNs+jh+gkK8gB8Lf05qL/O7KWg==", + "license": "MIT" + }, + "node_modules/@chevrotain/cst-dts-gen": { + "version": "11.0.3", + "resolved": "https://registry.npmjs.org/@chevrotain/cst-dts-gen/-/cst-dts-gen-11.0.3.tgz", + "integrity": 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+ "resolved": "https://registry.npmjs.org/marked/-/marked-13.0.3.tgz", + "integrity": "sha512-rqRix3/TWzE9rIoFGIn8JmsVfhiuC8VIQ8IdX5TfzmeBucdY05/0UlzKaw0eVtpcN/OdVFpBk7CjKGo9iHJ/zA==", + "license": "MIT", + "bin": { + "marked": "bin/marked.js" + }, + "engines": { + "node": ">= 18" + } + }, "node_modules/mdast-util-definitions": { "version": "6.0.0", "resolved": "https://registry.npmjs.org/mdast-util-definitions/-/mdast-util-definitions-6.0.0.tgz", @@ -5937,6 +6915,35 @@ "node": ">= 8" } }, + "node_modules/mermaid": { + "version": "11.4.0", + "resolved": "https://registry.npmjs.org/mermaid/-/mermaid-11.4.0.tgz", + "integrity": "sha512-mxCfEYvADJqOiHfGpJXLs4/fAjHz448rH0pfY5fAoxiz70rQiDSzUUy4dNET2T08i46IVpjohPd6WWbzmRHiPA==", + "license": "MIT", + "dependencies": { + "@braintree/sanitize-url": "^7.0.1", + "@iconify/utils": "^2.1.32", + "@mermaid-js/parser": "^0.3.0", + "@types/d3": "^7.4.3", + "@types/dompurify": "^3.0.5", + "cytoscape": "^3.29.2", + "cytoscape-cose-bilkent": "^4.1.0", + 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"https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz", @@ -7375,6 +8388,22 @@ "pathe": "^1.1.2" } }, + "node_modules/points-on-curve": { + "version": "0.2.0", + "resolved": "https://registry.npmjs.org/points-on-curve/-/points-on-curve-0.2.0.tgz", + "integrity": "sha512-0mYKnYYe9ZcqMCWhUjItv/oHjvgEsfKvnUTg8sAtnHr3GVy7rGkXCb6d5cSyqrWqL4k81b9CPg3urd+T7aop3A==", + "license": "MIT" + }, + "node_modules/points-on-path": { + "version": "0.2.1", + "resolved": "https://registry.npmjs.org/points-on-path/-/points-on-path-0.2.1.tgz", + "integrity": "sha512-25ClnWWuw7JbWZcgqY/gJ4FQWadKxGWk+3kR/7kD0tCaDtPPMj7oHu2ToLaVhfpnHrZzYby2w6tUA0eOIuUg8g==", + "license": "MIT", + "dependencies": { + "path-data-parser": "0.1.0", + "points-on-curve": "0.2.0" + } + }, "node_modules/postcss": { "version": "8.4.47", "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.47.tgz", @@ -8116,6 +9145,12 @@ "node": ">=0.10.0" } }, + "node_modules/robust-predicates": { + "version": "3.0.2", + "resolved": "https://registry.npmjs.org/robust-predicates/-/robust-predicates-3.0.2.tgz", + "integrity": "sha512-IXgzBWvWQwE6PrDI05OvmXUIruQTcoMDzRsOd5CDvHCVLcLHMTSYvOK5Cm46kWqlV3yAbuSpBZdJ5oP5OUoStg==", + "license": "Unlicense" + }, "node_modules/rollup": { "version": "4.24.0", "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.24.0.tgz", @@ -8151,6 +9186,18 @@ "fsevents": "~2.3.2" } }, + "node_modules/roughjs": { + "version": "4.6.6", + "resolved": "https://registry.npmjs.org/roughjs/-/roughjs-4.6.6.tgz", + "integrity": "sha512-ZUz/69+SYpFN/g/lUlo2FXcIjRkSu3nDarreVdGGndHEBJ6cXPdKguS8JGxwj5HA5xIbVKSmLgr5b3AWxtRfvQ==", + "license": "MIT", + "dependencies": { + "hachure-fill": "^0.5.2", + "path-data-parser": "^0.1.0", + "points-on-curve": "^0.2.0", + "points-on-path": "^0.2.1" + } + }, "node_modules/run-parallel": { "version": "1.2.0", "resolved": "https://registry.npmjs.org/run-parallel/-/run-parallel-1.2.0.tgz", @@ -8174,6 +9221,12 @@ "queue-microtask": "^1.2.2" } }, + "node_modules/rw": { + "version": "1.3.3", + "resolved": "https://registry.npmjs.org/rw/-/rw-1.3.3.tgz", + "integrity": "sha512-PdhdWy89SiZogBLaw42zdeqtRJ//zFd2PgQavcICDUgJT5oW10QCRKbJ6bg4r0/UY2M6BWd5tkxuGFRvCkgfHQ==", + "license": "BSD-3-Clause" + }, "node_modules/safe-buffer": { "version": "5.2.1", "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.2.1.tgz", @@ -8678,6 +9731,12 @@ "inline-style-parser": "0.1.1" } }, + "node_modules/stylis": { + "version": "4.3.4", + "resolved": "https://registry.npmjs.org/stylis/-/stylis-4.3.4.tgz", + "integrity": "sha512-osIBl6BGUmSfDkyH2mB7EFvCJntXDrLhKjHTRj/rK6xLH0yuPrHULDRQzKokSOD4VoorhtKpfcfW1GAntu8now==", + "license": "MIT" + }, "node_modules/sucrase": { "version": "3.35.0", "resolved": "https://registry.npmjs.org/sucrase/-/sucrase-3.35.0.tgz", @@ -9007,6 +10066,15 @@ "url": "https://github.com/sponsors/wooorm" } }, + "node_modules/ts-dedent": { + "version": "2.2.0", + "resolved": "https://registry.npmjs.org/ts-dedent/-/ts-dedent-2.2.0.tgz", + 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a/package.json b/package.json index 18b4cd280..a589cd10c 100755 --- a/package.json +++ b/package.json @@ -18,6 +18,7 @@ "astro": "^4.15.3", "astro-icon": "^1.1.1", "html-escaper": "^3.0.3", + "mermaid": "^11.4.0", "rehype-autolink-headings": "^7.1.0", "rehype-slug": "^6.0.0", "sharp": "^0.32.5", diff --git a/src/components/mdx/Mermaid.astro b/src/components/mdx/Mermaid.astro new file mode 100644 index 000000000..7a49867ca --- /dev/null +++ b/src/components/mdx/Mermaid.astro @@ -0,0 +1,67 @@ +--- + +// https://xkonti.tech/blog/astro-mermaid-mdx/ + +export interface Props { + title?: string; +} +const { title = "" } = Astro.props; +--- + + +
+
{title}
+ +
Loading diagram...
+ +
+ + Source + +
+ +
+
+
\ No newline at end of file From 4f7b8a6524e7aa272aba710456181e3b93462ce7 Mon Sep 17 00:00:00 2001 From: Kevin F Date: Thu, 14 Nov 2024 12:18:39 +0100 Subject: [PATCH 2/2] Update tertiary color --- src/components/mdx/Mermaid.astro | 2 ++ src/content/docs/start-here/assays.mdx | 19 +++++++++++++++++++ 2 files changed, 21 insertions(+) diff --git a/src/components/mdx/Mermaid.astro b/src/components/mdx/Mermaid.astro index 7a49867ca..a2be294af 100644 --- a/src/components/mdx/Mermaid.astro +++ b/src/components/mdx/Mermaid.astro @@ -43,6 +43,8 @@ document.addEventListener("DOMContentLoaded", async () => { theme: "base", themeVariables: { primaryColor: "#2D3E50", + tertiaryColor: "#3b5169", + tertiaryTextColor: "white", primaryTextColor: "white", lineColor: "#1FC2A7" } diff --git a/src/content/docs/start-here/assays.mdx b/src/content/docs/start-here/assays.mdx index c55ab04ea..0cfd7de11 100644 --- a/src/content/docs/start-here/assays.mdx +++ b/src/content/docs/start-here/assays.mdx @@ -13,6 +13,25 @@ import { Steps } from '@astrojs/starlight/components'; import { Card } from '@astrojs/starlight/components'; import { FileTree } from '@astrojs/starlight/components'; +import Mermaid from '@components/mdx/Mermaid.astro' + + +```mermaid +flowchart TB + c1-->a2 + subgraph one + a1-->a2 + end + subgraph two + b1-->b2 + end + subgraph three + c1-->c2 + end + +``` + + Ok, I think I understand. The study is used to describe the overall experiment and the sample generation. Then the assays are used to describe the individual lab processes and the data generation!