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;
+ }