From 27fe376a58e7da7740051fbec0d45405bce224fb Mon Sep 17 00:00:00 2001 From: Kevin F Date: Wed, 6 Nov 2024 13:21:18 +0100 Subject: [PATCH] fix links, clean up --- .github/workflows/deploy.yml | 39 ++ CONTRIBUTING.md | 18 + LICENSE | 395 ++++++++++++++++++ README.md | 62 +-- astro.config.mts | 2 + src/components/AuthorCard.astro | 2 +- src/components/starlight/Footer.astro | 23 +- .../docs/arc-commander/before-we-start.mdx | 4 +- src/content/docs/arc-commander/branches.mdx | 2 +- src/content/docs/arc-commander/index.mdx | 12 +- .../docs/arc-validation/cqc-pipelines.md | 4 +- .../arc-validation/validation-packages.md | 2 +- src/content/docs/arcitect/arcitect-lfs.mdx | 2 +- src/content/docs/arcitect/index.mdx | 4 +- src/content/docs/arcitect/installation.mdx | 4 +- src/content/docs/core-concepts/arc.mdx | 12 +- .../datahub-data-publications-archigator.md | 6 +- .../datahub-data-publications-cqc.md | 10 +- .../datahub-data-publications-dois.md | 6 +- .../datahub-data-publications-status.md | 4 +- .../docs/datahub/data-publications/index.mdx | 14 +- .../docs/datahub/datahub-arc-commits.mdx | 2 +- .../datahub-arc-members-isa-contacts.md | 2 +- .../docs/datahub/datahub-arc-panel.mdx | 2 +- .../docs/datahub/datahub-arc-settings.md | 2 +- src/content/docs/datahub/datahub-arc-wiki.md | 2 +- src/content/docs/datahub/datahub-files.mdx | 4 +- src/content/docs/datahub/datahub-groups.mdx | 2 +- .../datahub/datahub-invite-collaborators.mdx | 2 +- .../docs/datahub/datahub-navigation.mdx | 6 +- src/content/docs/datahub/datahub-projects.mdx | 2 +- .../docs/datahub/datahub-working-together.mdx | 12 +- src/content/docs/datahub/index.mdx | 20 +- .../fundamentals/data-management-plan.mdx | 4 +- .../docs/fundamentals/data-publications.mdx | 15 +- .../docs/fundamentals/data-sharing.mdx | 16 +- .../fundamentals/electronic-lab-notebooks.mdx | 2 +- .../fundamentals/fair-data-principles.mdx | 8 +- src/content/docs/fundamentals/metadata.mdx | 8 +- .../ontology-service-landscape.mdx | 10 +- .../fundamentals/persistent-identifiers.mdx | 2 +- .../fundamentals/public-data-repositories.mdx | 10 +- .../fundamentals/research-data-management.mdx | 25 +- .../docs/fundamentals/version-control-git.mdx | 6 +- .../docs/guides/arc-adding-external-data.mdx | 2 +- .../arc-commander-quick-start-expert.md | 2 +- .../docs/guides/arc-commander-quick-start.mdx | 16 +- .../docs/guides/arc-enabling-platforms.md | 44 +- src/content/docs/guides/arc-locations.md | 4 +- .../guides/arc-syncing-recommendation.mdx | 2 +- .../docs/guides/arc-working-with-branches.mdx | 2 +- .../docs/guides/data-analysis/arc-galaxy.mdx | 2 +- src/content/docs/guides/dataplan.mdx | 4 +- .../docs/guides/git-troubleshooting.md | 4 +- src/content/docs/guides/metadata-quiz.mdx | 2 +- src/content/docs/guides/publication-to-arc.md | 6 +- src/content/docs/guides/publish-arc.mdx | 4 +- src/content/docs/guides/validate-arc.mdx | 2 +- src/content/docs/index.mdx | 4 +- .../start-here/{04-assays.mdx => assays.mdx} | 0 .../{08-complete.mdx => complete.mdx} | 0 ...c-scaffold.mdx => create-arc-scaffold.mdx} | 0 ...05-data-analysis.mdx => data-analysis.mdx} | 2 +- .../{06-datamap.mdx => datamap.mdx} | 0 ...02-investigation.mdx => investigation.mdx} | 0 .../start-here/{07-share.mdx => share.mdx} | 2 +- .../start-here/{03-study.mdx => study.mdx} | 0 .../docs/swate/add-building-blocks.mdx | 8 +- src/content/docs/swate/annotation-table.mdx | 6 +- src/content/docs/swate/building-blocks.mdx | 4 +- src/content/docs/swate/index.mdx | 4 +- .../swate/swate-template-contribution.mdx | 4 +- src/content/docs/swate/term-search.mdx | 6 +- src/content/docs/vault/arc-user-journey.mdx | 14 +- .../docs/vault/arcitect-quick-start-videos.md | 6 +- .../docs/vault/arcitect-quick-start.md | 8 +- src/content/docs/vault/faqs.md | 12 +- src/content/docs/vault/reproduce-reuse.md | 4 +- .../docs/vault/swate-quickstart-videos.md | 6 +- src/content/docs/vault/swate-quickstart.md | 8 +- src/content/docs/vault/swate-walkthrough.md | 10 +- todo.md | 17 - 82 files changed, 701 insertions(+), 311 deletions(-) create mode 100644 .github/workflows/deploy.yml create mode 100644 LICENSE rename src/content/docs/start-here/{04-assays.mdx => assays.mdx} (100%) rename src/content/docs/start-here/{08-complete.mdx => complete.mdx} (100%) rename src/content/docs/start-here/{01-create-arc-scaffold.mdx => create-arc-scaffold.mdx} (100%) rename src/content/docs/start-here/{05-data-analysis.mdx => data-analysis.mdx} (94%) rename src/content/docs/start-here/{06-datamap.mdx => datamap.mdx} (100%) rename src/content/docs/start-here/{02-investigation.mdx => investigation.mdx} (100%) rename src/content/docs/start-here/{07-share.mdx => share.mdx} (95%) rename src/content/docs/start-here/{03-study.mdx => study.mdx} (100%) delete mode 100644 todo.md diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 000000000..979b6df76 --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,39 @@ +name: Deploy to GitHub Pages + +on: + # Trigger the workflow every time you push to the `main` branch + # Using a different branch name? Replace `main` with your branchโ€™s name + push: + branches: [ main ] + # Allows you to run this workflow manually from the Actions tab on GitHub. + workflow_dispatch: + +# Allow this job to clone the repo and create a page deployment +permissions: + contents: read + pages: write + id-token: write + +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Checkout your repository using git + uses: actions/checkout@v4 + - name: Install, build, and upload your site + uses: withastro/action@v3 + # with: + # path: . # The root location of your Astro project inside the repository. (optional) + # node-version: 20 # The specific version of Node that should be used to build your site. Defaults to 20. (optional) + # package-manager: pnpm@latest # The Node package manager that should be used to install dependencies and build your site. Automatically detected based on your lockfile. (optional) + + deploy: + needs: build + runs-on: ubuntu-latest + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 20f31218a..c44bbde94 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,3 +1,21 @@ +# Where should i place my content? + +## Start here + +This is a place for content required for the recommended way to work with an ARC. + +## Guides + +Here you can place content for a specific topic or task. Do not place specific tools documentation here. + +## + +If you have a tool that is used in the context of an ARC, you can place the documentation here. + +## Core concepts + +Basic information about RDM, not necessary ARC related. + # Style Guide ## Use Starlight components diff --git a/LICENSE b/LICENSE new file mode 100644 index 000000000..52bd1459b --- /dev/null +++ b/LICENSE @@ -0,0 +1,395 @@ +Attribution 4.0 International + +======================================================================= + +Creative Commons Corporation ("Creative Commons") is not a law firm and +does not provide legal services or legal advice. Distribution of +Creative Commons public licenses does not create a lawyer-client or +other relationship. Creative Commons makes its licenses and related +information available on an "as-is" basis. Creative Commons gives no +warranties regarding its licenses, any material licensed under their +terms and conditions, or any related information. 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Except for the limited purpose of indicating that +material is shared under a Creative Commons public license or as +otherwise permitted by the Creative Commons policies published at +creativecommons.org/policies, Creative Commons does not authorize the +use of the trademark "Creative Commons" or any other trademark or logo +of Creative Commons without its prior written consent including, +without limitation, in connection with any unauthorized modifications +to any of its public licenses or any other arrangements, +understandings, or agreements concerning use of licensed material. For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. \ No newline at end of file diff --git a/README.md b/README.md index e09bf55fe..7c3bcd5b2 100644 --- a/README.md +++ b/README.md @@ -1,55 +1,27 @@ -# Starlight Starter Kit: Basics +# DataPLANT Knowledge Base -[![Built with Starlight](https://astro.badg.es/v2/built-with-starlight/tiny.svg)](https://starlight.astro.build) +[![CC BY 4.0][cc-by-shield]][cc-by] -``` -npm create astro@latest -- --template starlight -``` +Welcome to the [DataPLANT knowledge base](https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html)! ๐Ÿ‘‹ -[![Open in StackBlitz](https://developer.stackblitz.com/img/open_in_stackblitz.svg)](https://stackblitz.com/github/withastro/starlight/tree/main/examples/basics) -[![Open with CodeSandbox](https://assets.codesandbox.io/github/button-edit-lime.svg)](https://codesandbox.io/p/sandbox/github/withastro/starlight/tree/main/examples/basics) -[![Deploy to Netlify](https://www.netlify.com/img/deploy/button.svg)](https://app.netlify.com/start/deploy?repository=https://github.com/withastro/starlight&create_from_path=examples/basics) -[![Deploy with Vercel](https://vercel.com/button)](https://vercel.com/new/clone?repository-url=https%3A%2F%2Fgithub.com%2Fwithastro%2Fstarlight%2Ftree%2Fmain%2Fexamples%2Fbasics&project-name=my-starlight-docs&repository-name=my-starlight-docs) +This knowledge base combines articles on +- **fundamental** topics on research data management (RDM) and +- how **DataPLANT implements** these aspects to support plant researchers with RDM tools and services. -> ๐Ÿง‘โ€๐Ÿš€ **Seasoned astronaut?** Delete this file. Have fun! +## Feedback & Contribution -## ๐Ÿš€ Project Structure +The DataPLANT knowledge base is a community effort and improves with every feedback we receive from readers and users. +**Your contribution is highly appreciated** no matter how little it may seem! -Inside of your Astro + Starlight project, you'll see the following folders and files: +If you just want to ask a question, recommend missing topics or tutorials, raise awareness for inconsistencies, typos, missing links, errors in training materials or tutorials, feel free to -``` -. -โ”œโ”€โ”€ public/ -โ”œโ”€โ”€ src/ -โ”‚ โ”œโ”€โ”€ assets/ -โ”‚ โ”œโ”€โ”€ content/ -โ”‚ โ”‚ โ”œโ”€โ”€ docs/ -โ”‚ โ”‚ โ””โ”€โ”€ config.ts -โ”‚ โ””โ”€โ”€ env.d.ts -โ”œโ”€โ”€ astro.config.mjs -โ”œโ”€โ”€ package.json -โ””โ”€โ”€ tsconfig.json -``` +- submit a ticket to our [helpdesk](https://helpdesk.nfdi4plants.org/?topic=Documentation_KnowledgeBase), +- [open an issue](https://github.com/nfdi4plants/nfdi4plants.knowledgebase/issues/new/) at GitHub or +- write us an email. -Starlight looks for `.md` or `.mdx` files in the `src/content/docs/` directory. Each file is exposed as a route based on its file name. +For all other contributions, please refer to the [contribution guide](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/CONTRIBUTING.html). -Images can be added to `src/assets/` and embedded in Markdown with a relative link. +## License -Static assets, like favicons, can be placed in the `public/` directory. - -## ๐Ÿงž Commands - -All commands are run from the root of the project, from a terminal: - -| Command | Action | -| :------------------------ | :----------------------------------------------- | -| `npm install` | Installs dependencies | -| `npm run dev` | Starts local dev server at `localhost:4321` | -| `npm run build` | Build your production site to `./dist/` | -| `npm run preview` | Preview your build locally, before deploying | -| `npm run astro ...` | Run CLI commands like `astro add`, `astro check` | -| `npm run astro -- --help` | Get help using the Astro CLI | - -## ๐Ÿ‘€ Want to learn more? - -Check out [Starlightโ€™s docs](https://starlight.astro.build/), read [the Astro documentation](https://docs.astro.build), or jump into the [Astro Discord server](https://astro.build/chat). +This work is licensed under a +[Creative Commons Attribution 4.0 International License][cc-by]. \ No newline at end of file diff --git a/astro.config.mts b/astro.config.mts index 111991e2f..a8d3352c7 100644 --- a/astro.config.mts +++ b/astro.config.mts @@ -10,6 +10,8 @@ import icon from "astro-icon"; // https://astro.build/config export default defineConfig({ + site: "https://nfdi4plants.github.io", + base: '/nfdi4plants.knowledgebase', integrations: [ icon(), starlight({ diff --git a/src/components/AuthorCard.astro b/src/components/AuthorCard.astro index 89e52fe73..06c949c15 100644 --- a/src/components/AuthorCard.astro +++ b/src/components/AuthorCard.astro @@ -38,7 +38,7 @@ const {author} = Astro.props; author.data.socials && author.data.socials.length > 0 &&
{ - author.data.socials.map((social) => ( + author.data.socials.map((social: any) => ( diff --git a/src/components/starlight/Footer.astro b/src/components/starlight/Footer.astro index 3236192b3..0d6ce9f10 100644 --- a/src/components/starlight/Footer.astro +++ b/src/components/starlight/Footer.astro @@ -13,16 +13,19 @@ const authors: CollectionEntry<'authors'>[] = Astro.props.entry.data.authors ? a -
-

- Authors -

-
- {authors.map((author) => ( - - ))} -
-
+ { + authors.length > 0 && +
+

+ Authors +

+
+ {authors.map((author) => ( + + ))} +
+
+ }