Merge pull request #881 from NFDI4Chem/development

Development

.gitignore

@@ -14,4 +14,6 @@ npm-debug.log
 yarn-error.log
 /.idea
 /.vscode
-/resources/ops/kubernetes/secret.yml
+/resources/ops/kubernetes/secret.yml
+docs/.vitepress/dist
+docs/.vitepress/cache

docs/.vitepress/config.mjs

@@ -0,0 +1,161 @@
+import { defineConfig } from 'vitepress'
+
+// https://vitepress.dev/reference/site-config
+export default defineConfig({
+  title: "nmrXiv",
+  description: "FAIR, consensus-driven NMR data repository and computational platform",
+  ignoreDeadLinks: true,
+
+  themeConfig: {
+    logo:  { 
+      light: "/logo.svg",
+      dark: "/logo-dark.svg",
+      alt : "nmrXiv" 
+    },
+
+    siteTitle: "",
+
+    // https://vitepress.dev/reference/default-theme-config
+    nav: [
+      { text: 'Home', link: '/introduction/intro.md' },
+      { text: 'Guides', link: '/developer-guides/architecture.md' }
+    ],
+
+    sidebar: [
+      {
+        text: 'Getting Started',
+        items: [
+          { text: 'Overview', link: '/introduction/intro.md' },
+          { text: 'Data',
+            items: [
+              { text: 'File Formats', link: '/introduction/data/formats.md'},
+              { text: 'Ontologies', link: '/introduction/data/ontologies.md'},
+              { text: 'Schemas', link: '/introduction/data/schemas.md'},
+              { text: 'Exemplary Data', link: '/introduction/data/exemplary-data.md'}
+            ]
+          }
+        ],
+      },
+      {
+        text: 'Submission Guides',
+        items: [
+          { text: 'Data - Life cycle', link: '/submission-guides/data-lifecycle.md' },
+          { text: 'Registration', link: '/submission-guides/registration.md' },
+          { text: 'Data Models',
+            items: [
+              { text: 'Project', link: '/submission-guides/data-model/project.md'},
+              { text: 'Sample/Study', link: '/submission-guides/data-model/study.md'},
+              { text: 'Spectra Dataset', link: '/submission-guides/data-model/dataset.md'},
+              { text: 'Team', link: '/submission-guides/data-model/team.md'},
+              { text: 'Sharing', link: '/submission-guides/data-model/sharing.md'}
+            ]
+          },
+          { text: 'Submission Process',
+            items: [
+              { text: 'OAuth', link: '/developer-guides/configurations/oauth.md'},
+              { text: 'Storage', link: '/developer-guides/configurations/storage.md'}
+            ]
+          },
+          { text: 'Spectra', link: '/developer-guides/architecture.md' },
+          { text: 'Licenses', link: '/submission-guides/licenses.md' }
+        ],
+      },
+      {
+        text: 'Developers Guides',
+        items: [
+          { text: 'Architecture', link: '/developer-guides/architecture.md' },
+          { text: 'Installation',
+            items: [
+              { text: 'macOS', link: '/developer-guides/installation/mac.md'},
+              { text: 'Windows', link: '/developer-guides/installation/windows.md'},
+              { text: 'Ubuntu', link: '/developer-guides/installation/ubuntu.md'},
+              { text: 'Centos', link: '/developer-guides/installation/centos.md'},
+              { text: 'Development Workflow', link: '/developer-guides/installation/development-workflow.md'}
+            ]
+          },
+          { text: 'Configuration',
+            items: [
+              { text: 'OAuth', link: '/developer-guides/configurations/oauth.md'},
+              { text: 'Storage', link: '/developer-guides/configurations/storage.md'}
+            ]
+          },
+          { text: 'Deployment',
+            items: [
+              { text: 'CI/CD', link: '/developer-guides/deployment/ci-cd.md'},
+              { text: 'GKE', link: '/developer-guides/deployment/gke.md'},
+              { text: 'Helm', link: '/developer-guides/deployment/helm.md'},
+              { text: 'Production', link: '/developer-guides/deployment/production.md'},
+              { text: 'Environments', link: '/developer-guides/deployment/environment.md'}
+            ]
+          },
+          { text: 'Code Contribution Guidelines', link: '/developer-guides/code-contribution-guidelines.md' },
+          { text: 'API', link: '/developer-guides/api.md' }
+        ],
+      },
+      {
+        text: 'Advance Guides',
+        items: [
+          { text: 'NMRium', link: '/advanced-guides/nmrium/nmrium.md' },  
+          { text: 'NMR Repositories Overview',
+            items: [
+              { text: 'Background', link: '/advanced-guides/nmr-repositories/background.md'},
+              { text: 'Data Sanitisation and Missing Values', link: '/advanced-guides/nmr-repositories/sanitisation.md'},
+              { text: 'Dimensionality', link: '/advanced-guides/nmr-repositories/dimensionality.md'},
+              { text: 'Spectrometer Frequency', link: '/advanced-guides/nmr-repositories/frequency.md'},
+              { text: 'Atomic Nuclei', link: '/advanced-guides/nmr-repositories/nuclei.md'},
+              { text: 'Temperature', link: '/advanced-guides/nmr-repositories/temperature.md'},
+              { text: 'Solvent', link: '/advanced-guides/nmr-repositories/solvent.md'},
+              { text: 'Instruments', link: '/advanced-guides/nmr-repositories/instrument.md'},
+              { text: 'pH', link: '/advanced-guides/nmr-repositories/ph.md'},
+              { text: 'Organism', link: '/advanced-guides/nmr-repositories/organism.md'},
+              { text: 'Organism Part', link: '/advanced-guides/nmr-repositories/part.md'},
+              { text: 'Variant', link: '/advanced-guides/nmr-repositories/variant.md'}
+
+            ]
+          },
+          { text: 'Spectral Viewing and Processing', link: '/submission-guides/spectra.md' },
+          { text: 'Licenses', link: '/submission-guides/licenses.md' }
+        ],
+      },
+      {
+        text: 'Community',
+        items: [
+          { text: 'Training', link: '/community/training.md' },
+          { text: 'NMR MIChI Workshops in NFDI4Chem', link: '/community/workshops.md' },
+          { text: 'Media Kit', link: '/community/media-kit.md' }
+        ],
+      },
+      {
+        text: 'Contribution',
+        items: [
+          { text: 'nmrXiv App', link: '/contribution/nmrxiv.md' },
+          { text: 'nmrXiv Docs', link: '/contribution/nmrxiv-docs.md' },
+          { text: 'Contributors and Steering Committee', link: '/contribution//contributors.md' }
+        ],
+      },
+      {
+        text: 'Miscellaneous',
+        items: [
+          { text: 'Tour', link: '/miscellaneous/tour.md' },
+          { text: 'Shortcuts', link: '/miscellaneous/shortcuts.md' },
+        ],
+      },
+      {
+        text: 'License' , link: 'license.md',
+      },
+      {
+        text: 'FAQ', link: 'FAQs.md'
+      }
+    ],
+
+
+    socialLinks: [
+      { icon: 'github', link: 'https://github.com/NFDI4Chem/nmrxiv' }
+    ],
+
+    footer: {
+      message: 'Source code released under the MIT License | Data are provided under the Creative Commons Attribution (aka CC-BY 4.0) <br/> Funded by the <a href="https://www.dfg.de/en/index.jsp" style="color: blue" target="_blank">Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)</a> under the <a href="https://www.nfdi4chem.de/" style="color: blue" target="_blank">National Research Data Infrastructure – NFDI4Chem</a> – Projektnummer <b>441958208.</b>',
+      copyright: `© ${new Date().getFullYear()} nmrXiv, Inc. All rights reserved.`
+    }
+  }
+})

docs/.vitepress/theme/index.ts

@@ -0,0 +1,33 @@
+// https://vitepress.dev/guide/custom-theme
+import { h } from 'vue'
+import Theme from 'vitepress/theme'
+import './style.css'
+import { onMounted, watch, nextTick } from 'vue';
+import { useRoute } from 'vitepress';
+import mediumZoom from 'medium-zoom';
+
+export default {
+  extends: Theme,
+  Layout: () => {
+    return h(Theme.Layout, null, {
+      // https://vitepress.dev/guide/extending-default-theme#layout-slots
+    })
+  },
+  enhanceApp({ app, router, siteData }) {
+    // ...
+  },
+  setup() {
+    const route = useRoute();
+    const initZoom = () => {
+      // mediumZoom('[data-zoomable]', { background: 'var(--vp-c-bg)' }); 
+      mediumZoom('.main img', { background: 'var(--vp-c-bg)' });
+    };
+    onMounted(() => {
+      initZoom();
+    });
+    watch(
+      () => route.path,
+      () => nextTick(() => initZoom())
+    );
+  },
+}

docs/.vitepress/theme/style.css

@@ -0,0 +1,176 @@
+/**
+ * Customize default theme styling by overriding CSS variables:
+ * https://github.com/vuejs/vitepress/blob/main/src/client/theme-default/styles/vars.css
+ */
+
+/**
+ * Colors
+ *
+ * Each colors have exact same color scale system with 3 levels of solid
+ * colors with different brightness, and 1 soft color.
+ * 
+ * - `XXX-1`: The most solid color used mainly for colored text. It must
+ *   satisfy the contrast ratio against when used on top of `XXX-soft`.
+ *
+ * - `XXX-2`: The color used mainly for hover state of the button.
+ *
+ * - `XXX-3`: The color for solid background, such as bg color of the button.
+ *   It must satisfy the contrast ratio with pure white (#ffffff) text on
+ *   top of it.
+ *
+ * - `XXX-soft`: The color used for subtle background such as custom container
+ *   or badges. It must satisfy the contrast ratio when putting `XXX-1` colors
+ *   on top of it.
+ *
+ *   The soft color must be semi transparent alpha channel. This is crucial
+ *   because it allows adding multiple "soft" colors on top of each other
+ *   to create a accent, such as when having inline code block inside
+ *   custom containers.
+ *
+ * - `default`: The color used purely for subtle indication without any
+ *   special meanings attched to it such as bg color for menu hover state.
+ *
+ * - `brand`: Used for primary brand colors, such as link text, button with
+ *   brand theme, etc.
+ *
+ * - `tip`: Used to indicate useful information. The default theme uses the
+ *   brand color for this by default.
+ *
+ * - `warning`: Used to indicate warning to the users. Used in custom
+ *   container, badges, etc.
+ *
+ * - `danger`: Used to show error, or dangerous message to the users. Used
+ *   in custom container, badges, etc.
+ * -------------------------------------------------------------------------- */
+
+ :root {
+    --vp-c-default-1: var(--vp-c-gray-1);
+    --vp-c-default-2: var(--vp-c-gray-2);
+    --vp-c-default-3: var(--vp-c-gray-3);
+    --vp-c-default-soft: var(--vp-c-gray-soft);
+
+    --vp-c-brand-1: var(--vp-c-indigo-1);
+    --vp-c-brand-2: var(--vp-c-indigo-2);
+    --vp-c-brand-3: var(--vp-c-indigo-3);
+    --vp-c-brand-soft: var(--vp-c-indigo-soft);
+
+    --vp-c-tip-1: var(--vp-c-brand-1);
+    --vp-c-tip-2: var(--vp-c-brand-2);
+    --vp-c-tip-3: var(--vp-c-brand-3);
+    --vp-c-tip-soft: var(--vp-c-brand-soft);
+
+    --vp-c-warning-1: var(--vp-c-yellow-1);
+    --vp-c-warning-2: var(--vp-c-yellow-2);
+    --vp-c-warning-3: var(--vp-c-yellow-3);
+    --vp-c-warning-soft: var(--vp-c-yellow-soft);
+
+    --vp-c-danger-1: var(--vp-c-red-1);
+    --vp-c-danger-2: var(--vp-c-red-2);
+    --vp-c-danger-3: var(--vp-c-red-3);
+    --vp-c-danger-soft: var(--vp-c-red-soft);
+  }
+
+  /**
+   * Component: Button
+   * -------------------------------------------------------------------------- */
+
+  :root {
+    --vp-button-brand-border: transparent;
+    --vp-button-brand-text: var(--vp-c-white);
+    --vp-button-brand-bg: var(--vp-c-brand-3);
+    --vp-button-brand-hover-border: transparent;
+    --vp-button-brand-hover-text: var(--vp-c-white);
+    --vp-button-brand-hover-bg: var(--vp-c-brand-2);
+    --vp-button-brand-active-border: transparent;
+    --vp-button-brand-active-text: var(--vp-c-white);
+    --vp-button-brand-active-bg: var(--vp-c-brand-1);
+  }
+
+  /**
+   * Component: Home
+   * -------------------------------------------------------------------------- */
+
+  :root {
+    --vp-home-hero-name-color: transparent;
+    --vp-home-hero-name-background: -webkit-linear-gradient(
+      120deg,
+      #bd34fe 30%,
+      #41d1ff
+    );
+
+    --vp-home-hero-image-background-image: linear-gradient(
+      -45deg,
+      #bd34fe 50%,
+      #47caff 50%
+    );
+    --vp-home-hero-image-filter: blur(40px);
+  }
+
+  @media (min-width: 640px) {
+    :root {
+      --vp-home-hero-image-filter: blur(56px);
+    }
+  }
+
+  @media (min-width: 960px) {
+    :root {
+      --vp-home-hero-image-filter: blur(72px);
+    }
+  }
+
+  /**
+   * Component: Custom Block
+   * -------------------------------------------------------------------------- */
+
+  :root {
+    --vp-custom-block-tip-border: transparent;
+    --vp-custom-block-tip-text: var(--vp-c-text-1);
+    --vp-custom-block-tip-bg: var(--vp-c-brand-soft);
+    --vp-custom-block-tip-code-bg: var(--vp-c-brand-soft);
+  }
+
+  /**
+   * Component: Algolia
+   * -------------------------------------------------------------------------- */
+
+  .DocSearch {
+    --docsearch-primary-color: var(--vp-c-brand-1) !important;
+  }
+
+  .VPHomeHero .text{
+    font-size: 36px !important;
+    line-height: 42px !important;
+  }
+
+  .name{
+    font-size: 64px !important;
+    line-height: 84px !important;
+  }
+
+  .logo{
+    height: 36px !important;
+  }
+
+  html img.only-on-dark {
+    display: none;
+  }
+
+  html img.only-on-light {
+    display: block;
+  }
+
+  html.dark img.only-on-light {
+    display: none;
+  }
+
+  html.dark img.only-on-dark {
+    display: block;
+  }
+
+  .medium-zoom-overlay {
+    z-index: 100;
+  }
+
+  .medium-zoom-image {
+    z-index: 100;
+  }