fix links, clean up

.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 branch’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

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.
+
+## <specific-tool>
+
+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

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)! 👋
 
-[![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.
 
-> 🧑‍🚀 **Seasoned astronaut?** Delete this file. Have fun!
+## Feedback & Contribution
 
-## 🚀 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
 
-```
-.
-├── public/
-├── src/
-│   ├── assets/
-│   ├── content/
-│   │   ├── docs/
-│   │   └── config.ts
-│   └── env.d.ts
-├── astro.config.mjs
-├── package.json
-└── 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 <a href="javascript:location='mailto:\u0069\u006e\u0066\u006f\u0040\u006e\u0066\u0064\u0069\u0034\u0070\u006c\u0061\u006e\u0074\u0073\u002e\u006f\u0072\u0067';void 0">email</a>.
 
-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.
-
-## 🧞 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                     |
-
-## 👀 Want to learn more?
-
-Check out [Starlight’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].

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({

src/components/AuthorCard.astro

@@ -38,7 +38,7 @@ const {author} = Astro.props;
       author.data.socials && author.data.socials.length > 0 &&
         <div class="flex grow items-center gap-2">
             {
-              author.data.socials.map((social) => (
+              author.data.socials.map((social: any) => (
                 <a href={social.href} target="_blank" class="w-7 h-7">
                   <Icon name={social.icon} class="w-7 h-7 simpleIcons" title={social.icon.split(":")[1]}/>
                 </a>

src/components/starlight/Footer.astro

@@ -13,16 +13,19 @@ const authors: CollectionEntry<'authors'>[] = Astro.props.entry.data.authors ? a
   <Default {...Astro.props}>
     <slot />
   </Default>
-  <div>
-    <p class="text-lg text">
-      Authors
-    </p>
-    <div class="flex flex-col gap-2 md:gap-4">
-      {authors.map((author) => (
-        <AuthorCard author={author} />
-      ))}
-    </div>
-  </div>
+  {
+    authors.length > 0 &&
+      <div>
+        <p class="text-lg text">
+          Authors
+        </p>
+        <div class="flex flex-col gap-2 md:gap-4">
+          {authors.map((author) => (
+            <AuthorCard author={author} />
+          ))}
+        </div>
+      </div>
+  }
 </footer>
 
 <style>

src/content/docs/arc-commander/before-we-start.mdx

@@ -7,7 +7,7 @@ lastUpdated: 2023-06-14
 After the setup steps, you're all set and ready to start using the ARC Commander. 🎉
 
 :::tip
-We recommend trying the [ARC Commander QuickStart](/guides/arc-commander-quick-start) for your first steps with the ARC Commander. 
+We recommend trying the [ARC Commander QuickStart](/nfdi4plants.knowledgebase/guides/arc-commander-quick-start) for your first steps with the ARC Commander. 
 :::
 
 :::tip
@@ -17,7 +17,7 @@ After the quickstarts, we strongly recommend to read the in-depth ARC Commander
 
 ## Notes on ARC Commander Guides
 
-- For most steps in this manual and in the [ARC Commander QuickStart](/guides/arc-commander-quick-start), it is assumed, that you opened a [shell or command prompt](/guides/tutorial-command-line) within a directory you want to initiate as an ARC
+- For most steps in this manual and in the [ARC Commander QuickStart](/nfdi4plants.knowledgebase/guides/arc-commander-quick-start), it is assumed, that you opened a [shell or command prompt](/nfdi4plants.knowledgebase/guides/tutorial-command-line) within a directory you want to initiate as an ARC
 - In the shell, `arc` defines the path to the ARC Commander executable (e.g. on Windows "C:\Users\userA\programs\ArcCommander\arc.exe").
 - Note that each input that contains non-literal characters must be encapsulated in "quotation marks" when entered within the shell. This also applies when using the editor for numerals that are no numbers (dates, phone numbers, etc.).
 

src/content/docs/arc-commander/branches.mdx

@@ -5,7 +5,7 @@ title: "Working on an ARC branch"
 
 ## Challenge
 
-- No direct access rights to the main branch (which can be handled via the [DataHUB](/datahub)) or 
+- No direct access rights to the main branch (which can be handled via the [DataHUB](/nfdi4plants.knowledgebase/datahub)) or 
 - Many people working on the same repository, making direct pushing to main branch chaotic.
 
 ## Solution

src/content/docs/arc-commander/index.mdx

@@ -20,19 +20,19 @@ Please check out the [ARC Commander Dev Docs](https://nfdi4plants.github.io/arcC
 
 The ARC Commander supports you in many actions on files within your ARC enabling you to sort, associate and keep track of your files.
 
-The major function of the ARC Commander is to set up the ARC directory and put it under [version-control](/fundamentals/version-control-git) for you. The ARC Commander creates the directory structure with the root directories "studies", "assays", "runs", and "workflows" (see [ARC](/core-concepts/arc) for details).  According to the design of your project, you can use the ARC Commander to create study and assay sub-directories and add the associated details and data files. While setting up the root directory structure, the ARC Commander initializes your ARC as a [git](/fundamentals/version-control-git) repository, allowing you to track changes of your ARC and easily back-up and synchronize it with the [DataHUB](/datahub). This includes an efficient mechanism to keep track of your large data files. The ARC Commander makes it straight-forward to download shared ARCs from the DataHUB for collaboration.
+The major function of the ARC Commander is to set up the ARC directory and put it under [version-control](/nfdi4plants.knowledgebase/fundamentals/version-control-git) for you. The ARC Commander creates the directory structure with the root directories "studies", "assays", "runs", and "workflows" (see [ARC](/nfdi4plants.knowledgebase/core-concepts/arc) for details).  According to the design of your project, you can use the ARC Commander to create study and assay sub-directories and add the associated details and data files. While setting up the root directory structure, the ARC Commander initializes your ARC as a [git](/nfdi4plants.knowledgebase/fundamentals/version-control-git) repository, allowing you to track changes of your ARC and easily back-up and synchronize it with the [DataHUB](/nfdi4plants.knowledgebase/datahub). This includes an efficient mechanism to keep track of your large data files. The ARC Commander makes it straight-forward to download shared ARCs from the DataHUB for collaboration.
 
-Apart from managing the ARC as a whole in terms of file handling, the ARC Commander supervises the integrity and connections between files of your ARC. It ensures that the ARC is intact following the [ARC specifications](/core-concepts/arc/#arc-specification) as well as the ISA model to provide machine-readability of metadata. By (automatically) registering your studies and assays including their associated meta(data) files in the `isa.investigation.xlsx` registry file, the ARC Commander makes the resources in your ARC identifiable and findable. It would also warn you about possible inconsistencies, such as duplicate ISA metadata files (e.g. every ARC stores only one `isa.investigation.xlsx`) or studies and assays that may have been added manually and not registered, yet.
+Apart from managing the ARC as a whole in terms of file handling, the ARC Commander supervises the integrity and connections between files of your ARC. It ensures that the ARC is intact following the [ARC specifications](/nfdi4plants.knowledgebase/core-concepts/arc/#arc-specification) as well as the ISA model to provide machine-readability of metadata. By (automatically) registering your studies and assays including their associated meta(data) files in the `isa.investigation.xlsx` registry file, the ARC Commander makes the resources in your ARC identifiable and findable. It would also warn you about possible inconsistencies, such as duplicate ISA metadata files (e.g. every ARC stores only one `isa.investigation.xlsx`) or studies and assays that may have been added manually and not registered, yet.
 
 ## What the ARC Commander does not do
 
-Unless you actively request it to, the ARC Commander does not delete, modify or move files within your ARC. While it may help with suggestions, the ARC Commander will not guess your intentions or override your decisions. For instance, the ARC Commander will not search any (ISA) metadata or other data files in your ARC and move them into the intended folders. If such files exist somewhere in your ARC, they will simply be ignored as "additional payload" (see [ARC specifications](/core-concepts/arc/#arc-specification)). The ARC Commander does not operate / manage your ARC automatically. You have the full control over all actions. Whenever you decide to add or link new (meta)data in your ARC or synchronize it with the [DataHUB](/datahub), you can do so with a few commands.
+Unless you actively request it to, the ARC Commander does not delete, modify or move files within your ARC. While it may help with suggestions, the ARC Commander will not guess your intentions or override your decisions. For instance, the ARC Commander will not search any (ISA) metadata or other data files in your ARC and move them into the intended folders. If such files exist somewhere in your ARC, they will simply be ignored as "additional payload" (see [ARC specifications](/nfdi4plants.knowledgebase/core-concepts/arc/#arc-specification)). The ARC Commander does not operate / manage your ARC automatically. You have the full control over all actions. Whenever you decide to add or link new (meta)data in your ARC or synchronize it with the [DataHUB](/nfdi4plants.knowledgebase/datahub), you can do so with a few commands.
 
 
 ## Do I have to use the ARC Commander?
 
-No. As with most tools and services developed in DataPLANT, you are not obliged to use the ARC Commander to benefit from DataPLANT's support in [FAIR RDM](/fundamentals/research-data-management).
-However, we'd highly recommend to check it following the [ARC Commander QuickStart](/guides/arc-commander-quick-start).
+No. As with most tools and services developed in DataPLANT, you are not obliged to use the ARC Commander to benefit from DataPLANT's support in [FAIR RDM](/nfdi4plants.knowledgebase/fundamentals/research-data-management).
+However, we'd highly recommend to check it following the [ARC Commander QuickStart](/nfdi4plants.knowledgebase/guides/arc-commander-quick-start).
 
 The alternative would be to
 
@@ -48,7 +48,7 @@ The ARC Commander runs on current Windows, Mac and Linux operating systems. The
 
 For details, please
 
-- try out the [ARC Commander QuickStart](/guides/arc-commander-quick-start),
+- try out the [ARC Commander QuickStart](/nfdi4plants.knowledgebase/guides/arc-commander-quick-start),
 - check the [GitHub repository](https://github.com/nfdi4plants/ARCCommander) to download and install the latest ARC Commander release on your device, or
 - explore this ARC Commander Manual for in-depth details.
 

src/content/docs/arc-validation/cqc-pipelines.md

@@ -23,6 +23,6 @@ The [ARC Validation Package Registry (AVPR)](https://avpr.nfdi4plants.org) is th
 
 ## Use Validation packages in your CQC pipeline
 
-_practical guide: [find and use ARC Validation Packages](/arc-validation/validation-packages)_
+_practical guide: [find and use ARC Validation Packages](/nfdi4plants.knowledgebase/arc-validation/validation-packages)_
 
-Users can choose to validate against any validation package available on the AVPR. To do so, they need to add the package and desired version to their ARC's `validation_packages.yml` file. The CQC pipeline will then automatically validate the ARC against the selected packages on every commit. The file can be created manually or by DataPLANT tooling such as the [ARCitect](/arcitect). For more information, visit the [practical guide](/arc-validation/validation-packages).
+Users can choose to validate against any validation package available on the AVPR. To do so, they need to add the package and desired version to their ARC's `validation_packages.yml` file. The CQC pipeline will then automatically validate the ARC against the selected packages on every commit. The file can be created manually or by DataPLANT tooling such as the [ARCitect](/nfdi4plants.knowledgebase/arcitect). For more information, visit the [practical guide](/nfdi4plants.knowledgebase/arc-validation/validation-packages).

src/content/docs/arc-validation/validation-packages.md

@@ -9,7 +9,7 @@ Users can choose to validate against any validation package available on the [AR
 
 To include a validation package in a PLANTDataHUB CQC pipeline, it has to be referenced in the `validation_packages.yml` file located in the `.arc` directory in the ARC's root directory. The file can be created manually or by DataPLANT tooling such as the ARCitect.
 
-Let's for example have a look at the **[invenio validation package](https://avpr.nfdi4plants.org/package/invenio)**, which an ARC must pass to be eligible for [data publication](/datahub/data-publications). The AVPR page states that (at the time of writing this guide) the latest version is `2.0.1` and that to include this package in the CQC pipeline, the following content has to be added to the `validation_packages.yml` file:
+Let's for example have a look at the **[invenio validation package](https://avpr.nfdi4plants.org/package/invenio)**, which an ARC must pass to be eligible for [data publication](/nfdi4plants.knowledgebase/datahub/data-publications). The AVPR page states that (at the time of writing this guide) the latest version is `2.0.1` and that to include this package in the CQC pipeline, the following content has to be added to the `validation_packages.yml` file:
 
 ```yaml
 validation_packages:

src/content/docs/arcitect/arcitect-lfs.mdx

@@ -39,5 +39,5 @@ or you can also choose to download all large files from a directory by right cli
 ![](@images/arcitect/arcitect-download-lfs-from-directory.drawio.png)
 
 :::tip
-If you use **[ARCitect](/arcitect)** to manage your ARCs, make sure to select or unselect the boxes `LFS` (in the "Download ARC" panel) or `Download LFS Files` (in the "Versions" panel) in order to allow or prevent syncing large files (LFS = large file storage).
+If you use **[ARCitect](/nfdi4plants.knowledgebase/arcitect)** to manage your ARCs, make sure to select or unselect the boxes `LFS` (in the "Download ARC" panel) or `Download LFS Files` (in the "Versions" panel) in order to allow or prevent syncing large files (LFS = large file storage).
 :::

src/content/docs/arcitect/index.mdx

@@ -5,8 +5,8 @@ lastUpdated: 2023-11-02
 
 Welcome to the ARCitect Manual.
 
-- Please install the ARCitect following [these instructions](/arcitect/installation)
-- The guide [Start Here](/start-here) introduces the major ARCitect functions
+- Please install the ARCitect following [these instructions](/nfdi4plants.knowledgebase/arcitect/installation)
+- The guide [Start Here](/nfdi4plants.knowledgebase/start-here) introduces the major ARCitect functions
 
 :::tip
 After installation, please check the ARCitect's help menu for further documentation and guides.