Merge pull request #534 from nfdi4plants/arccommander-menu

Arccommander-menu

astro.config.mts

@@ -89,7 +89,6 @@ export default defineConfig({
         {
           label: 'DataHUB',
           collapsed: true,
-          // autogenerate: { directory: 'datahub' },
           items:[
             'datahub',           
             {
@@ -123,7 +122,28 @@ export default defineConfig({
           label: 'ARC Commander',
           // Collapse the group by default.
           collapsed: true,
-          autogenerate: { directory: 'arc-commander' },
+          items:[
+            'arc-commander',           
+            {
+              label: 'Setup',
+              collapsed: false,
+              autogenerate: { directory: 'arc-commander/setup'},
+            },
+            'arc-commander/before-we-start',
+            'arc-commander/arc-commander-quick-start',
+            'arc-commander/arc-commander-quick-start-expert',
+            {
+              label: 'Central Functions',
+              collapsed: false,
+              autogenerate: { directory: 'arc-commander/central-functions'},
+            },
+            {
+              label: 'ISA metadata',
+              collapsed: false,
+              autogenerate: { directory: 'arc-commander/isa'},
+            },
+            'arc-commander/lfs',
+          ]
         },
         {
           label: 'Swate',

src/content/docs/arc-commander/arc-commander-quick-start-expert.md

@@ -4,6 +4,8 @@ lastUpdated: 2023-01-27
 authors:
   - dominik-brilhaus
 pagefind: false 
+sidebar:
+  order: 4.6
 ---
 
 ## About this guide

src/content/docs/arc-commander/arc-commander-quick-start.mdx

@@ -4,6 +4,8 @@ authors:
   - martin-kuhl
   - dominik-brilhaus
 lastUpdated: 2023-06-09
+sidebar:
+  order: 4.5
 ---
 
 import NewARC from '@components/mdx/NewARC.mdx'
@@ -14,7 +16,7 @@ In this guide we focus on how to use the [ARC Commander][def] to create your ARC
 
 ## Before we can start
 
-☑️ Please [install ARC Commander](/nfdi4plants.knowledgebase/arc-commander/installation)
+☑️ Please [install ARC Commander](/nfdi4plants.knowledgebase/arc-commander/setup/installation)
 ☑️ Find <a href="/nfdi4plants.knowledgebase/arc-commander/tutorial-command-line" target="_blank">the command line</a> on your system  
 💡 Consider reading about [ARC](/nfdi4plants.knowledgebase/core-concepts/arc) and the [ARC Commander][def]  
 💡 After concluding this quickstart, consider exploring the [ARC Commander manual][def] for a more detailed usage instruction.

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

@@ -1,10 +1,11 @@
 ---
-title: "Before we start"
+title: Before we start
 lastUpdated: 2023-06-14
+sidebar:
+  order: 4
 ---
 
-
-After the setup steps, you're all set and ready to start using the ARC Commander. 🎉
+After the setup, you're all set and ready to start using the ARC Commander. 🎉
 
 :::tip
 We recommend trying the [ARC Commander QuickStart](/nfdi4plants.knowledgebase/arc-commander/arc-commander-quick-start) for your first steps with the ARC Commander. 

src/content/docs/arc-commander/branches.mdx → src/content/docs/arc-commander/central-functions/branches.mdx

@@ -1,8 +1,9 @@
 ---
 title: "Working on an ARC branch"
+sidebar:
+  order: 10
 ---
 
-
 ## Challenge
 
 - No direct access rights to the main branch (which can be handled via the [DataHUB](/nfdi4plants.knowledgebase/datahub)) or 

src/content/docs/arc-commander/config.mdx → src/content/docs/arc-commander/central-functions/config.mdx

@@ -1,6 +1,8 @@
 ---
 title: Config User
 lastUpdated: 2022-12-13
+sidebar:
+  order: 9
 ---
 
 

src/content/docs/arc-commander/connect.mdx → src/content/docs/arc-commander/central-functions/connect.mdx

@@ -1,6 +1,8 @@
 ---
 title: "Connect an ARC to the DataHUB"
 lastUpdated: 2022-12-13
+sidebar:
+  order: 7
 ---
 
 In case you have not yet connected your local repository to a remote one, you can specify the remote repository with the flag `--repositoryaddress` or `-r` in combination with a URL + ".git", e.g.,

src/content/docs/arc-commander/get.mdx → src/content/docs/arc-commander/central-functions/get.mdx

@@ -1,15 +1,17 @@
 ---
-title: "Clone an ARC from the DataHUB"
+title: Clone an ARC from the DataHUB
 lastUpdated: 2022-12-20
 authors:
   - martin-kuhl
+sidebar:
+  order: 6
 ---
 
 
 Using `arc get -r` followed by a URL + ".git" enables you to clone an already existing ARC as a local repository, e.g.,
 
 ```bash
-arc get -r https://github.com/nfdi4plants/ARC.git
+arc get -r https://git.nfdi4plants.org/muehlhaus/ArcPrototype
 ```
 
 :::tip

src/content/docs/arc-commander/initialization.mdx → src/content/docs/arc-commander/central-functions/initialization.mdx

@@ -1,6 +1,8 @@
 ---
-title: "Initialize an ARC"
+title: Initialize an ARC
 lastUpdated: 2022-12-13
+sidebar:
+  order: 5
 ---
 
 - The basic ARC folder structure can be created using `arc init`

src/content/docs/arc-commander/synchronization.mdx → src/content/docs/arc-commander/central-functions/synchronization.mdx

@@ -1,6 +1,8 @@
 ---
 title: "Sychronize an ARC"
 lastUpdated: 2022-12-13
+sidebar:
+  order: 8
 ---
 
 The command `arc sync` handles multiple operations for your ARC in one step. It will

src/content/docs/arc-commander/export.mdx → src/content/docs/arc-commander/isa/export.mdx

@@ -3,6 +3,8 @@ title: "Export ARC metadata"
 lastUpdated: 2022-12-20
 authors:
   - martin-kuhl
+sidebar:
+  order: 15
 ---
 
 

src/content/docs/arc-commander/isa-assay.mdx → src/content/docs/arc-commander/isa/isa-assay.mdx

@@ -1,6 +1,8 @@
 ---
 title: "Assay"
 lastUpdated: 2022-12-13
+sidebar:
+  order: 13
 ---
 
 ## Addition of assays

src/content/docs/arc-commander/isa-investigation.mdx → src/content/docs/arc-commander/isa/isa-investigation.mdx

@@ -1,6 +1,8 @@
 ---
 title: "Investigation"
 lastUpdated: 2022-12-13
+sidebar:
+  order: 11
 ---
 
 :::caution

src/content/docs/arc-commander/isa-study.mdx → src/content/docs/arc-commander/isa/isa-study.mdx

@@ -1,8 +1,8 @@
 ---
 title: "Study"
 lastUpdated: 2022-12-13
-tableOfContents:
-  maxHeadingLevel: 4
+sidebar:
+  order: 12
 ---
 
 :::caution

src/content/docs/arc-commander/update.mdx → src/content/docs/arc-commander/isa/isa-update.mdx

@@ -1,8 +1,9 @@
 ---
 title: "Update ISA metadata"
 lastUpdated: 2022-12-21
+sidebar:
+  order: 14
 ---
-
 Users have the possibility to update the metadata in the isa.investigation.xlsx by filling it with metadata from the study and assay files in the respective subdirectories via the command
 
 ```bash

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

@@ -3,6 +3,8 @@ title: Large File Storage (LFS)
 lastUpdated: 2024-10-31
 author:
 - dominik-brilhaus
+sidebar:
+  order: 16
 ---
 
 

src/content/docs/arc-commander/access.mdx → src/content/docs/arc-commander/setup/access.mdx

@@ -5,6 +5,8 @@ author:
 - martin-kuhl
 - dominik-brilhaus
 - david-zimmer
+sidebar:
+  order: 3
 ---
 
 

src/content/docs/arc-commander/installation-git.mdx → src/content/docs/arc-commander/setup/installation-git.mdx

@@ -1,9 +1,12 @@
 ---
 title: Installation of Git and Git LFS
 lastUpdated: 2023-11-24
+author:
+    - dominik-brilhaus
+sidebar:
+  order: 1
 ---
 
-
 In order to use the ARC Commander, Git (version ≥ 2.32.0) and Git LFS must be installed on your computer.
 
 :::tip

src/content/docs/arc-commander/installation.mdx → src/content/docs/arc-commander/setup/installation.mdx

@@ -1,6 +1,8 @@
 ---
 title: "Installing the ARC Commander"
 lastUpdated: 2022-12-20
+sidebar:
+  order: 2
 ---
 import { Steps } from '@astrojs/starlight/components';
 import { Tabs, TabItem } from '@astrojs/starlight/components';

src/content/docs/git/git-syncing-recommendation.mdx

@@ -21,7 +21,7 @@ In DataPLANT tools and services, the individual sync steps are called "commit".
 ## Add a message to communicate your ARC's evolution
 
 We recommend adding a message that shortly summarizes, what you did since you last synced your ARC.
-Commit messages can be added via [ARCitect's](/nfdi4plants.knowledgebase/arcitect) commit menu or via [ARC commander](/nfdi4plants.knowledgebase/arc-commander/synchronization).
+Commit messages can be added via [ARCitect's](/nfdi4plants.knowledgebase/arcitect) commit menu or via [ARC commander](/nfdi4plants.knowledgebase/arc-commander/central-functions/synchronization).
 
 The following exemplifies Viola's commit messages along with the progress of her ARC:
 

src/content/docs/git/git-troubleshooting.md

@@ -15,8 +15,8 @@ authors:
 Some reasons, why we now sometimes run into git issues
 
 - Over the past years we asked users (e.g. during trainings) to install git with minium required guidance
-- Even though more advanced tools (ARCitect) now bring their own git installation, there might still occur interferences with older installations
-- There might also be issues of tools (e.g. ARCitect and ARC commander) or different versions of those tools handling git-related tasks a bit differently or more / less strict (e.g. things like `main` as the default branch)
+- Even though more advanced tools ([ARCitect](/nfdi4plants.knowledgebase/arcitect/)) now bring their own git installation, there might still occur interferences with older installations
+- There might also be issues of tools (e.g. [ARCitect](/nfdi4plants.knowledgebase/arcitect/) and [ARC commander](/nfdi4plants.knowledgebase/arc-commander/)) or different versions of those tools handling git-related tasks a bit differently or more / less strict (e.g. things like `main` as the default branch)
 - The current (versions of) tools were not really built for collaboration with many people on one ARC (at least not with default settings from DataHUB side). So common errors are related to merge conflicts (multiple users changing files) and divergent branches (e.g. between local and remote clones of the ARC).
 - Some behaviors are simply very use-case or setup specific and will in any case and even with the best tooling require some stewardship
 
@@ -34,6 +34,7 @@ Some reasons, why we now sometimes run into git issues
 - On macOS: right-click ARC folder-->"Services"--> "New Terminal at Folder"
 - On windows: open folder via Explorer; type "cmd" or "powershell" into the address field on top of Explorer
 - On linux / macOS terminal: `cd path/to/ARC`
+- From inside ARCitect: Tools -> Command Window
 
 3. try some of the git commands and debugging below
 
@@ -266,7 +267,7 @@ It usually helps to just retrieve new ones. If not, you might have to remove exi
 
 #### Authenticate the computer
 
-Option 1: [via ARC Commander](/nfdi4plants.knowledgebase/arc-commander/access)
+Option 1: [via ARC Commander](/nfdi4plants.knowledgebase/arc-commander/setup/access)
 
 Option 2: "by hand"
   1. Login to the [DataHUB](https://git.nfdi4plants.org/)

src/content/docs/git/git-working-with-branches.mdx

@@ -25,6 +25,6 @@ import ARCitectBranches from '../arcitect/arcitect-branches.mdx'
 
 ## ARC Commander
 
-import ARCCommanderBranches from '../arc-commander/branches.mdx'
+import ARCCommanderBranches from '../arc-commander/central-functions/branches.mdx'
 
 <ARCCommanderBranches />

src/content/docs/vault/faqs.md

@@ -98,15 +98,15 @@ Why do I get the error `'arc' is not recognized as an internal or external comma
 
 Your machine cannot find your ARC commander executable. Possible reasons are that you have not yet installed the ARC commander or that the `arc` executable was not added to your path. 
 
-Please carefully retry the [ARC Commander setup](/nfdi4plants.knowledgebase/arc-commander/installation). 
+Please carefully retry the [ARC Commander setup](/nfdi4plants.knowledgebase/arc-commander/setup/installation). 
 
 If this does not do the trick, please follow these steps towards debugging (on Windows): 
 
 1. Open the command prompt (cmd) or powershell in the folder (e.g. `C:\Programs\ArcCommander`) where you stored the ARC Commander program (e.g. arc.exe). If `arc --version` shows the version, the executable is intact. 
 2. Next, execute `path` to check wether the folder (e.g. `C:\Programs\ArcCommander`) appears in your path.
 3. Adapt the user's path (not admin)
 
-:bulb: If you do not have admin rights on the computer, please open the settings "Edit environment variables for your account" and follow steps described in the [ARC Commander setup](/nfdi4plants.knowledgebase/arc-commander/installation).
+:bulb: If you do not have admin rights on the computer, please open the settings "Edit environment variables for your account" and follow steps described in the [ARC Commander setup](/nfdi4plants.knowledgebase/arc-commander/setup/installation).
 
 </details>