rename git org (#750)

.github/workflows/backend.yml

@@ -4,7 +4,7 @@ on:
   push:
 
 env:
-  DOCKER_IMAGE_NAME: ghcr.io/pathoplexus/backend
+  DOCKER_IMAGE_NAME: ghcr.io/loculus-project/backend
 
 defaults:
   run:

.github/workflows/dummyPreprocessing.yml

@@ -4,7 +4,7 @@ on:
   push:
 
 env:
-  DOCKER_IMAGE_NAME: ghcr.io/pathoplexus/preprocessing-dummy
+  DOCKER_IMAGE_NAME: ghcr.io/loculus-project/preprocessing-dummy
 
 defaults:
   run:

.github/workflows/preprocessing-nextclade.yaml

@@ -4,7 +4,7 @@ on:
   push:
 
 env:
-  DOCKER_IMAGE_NAME: ghcr.io/pathoplexus/preprocessing-nextclade
+  DOCKER_IMAGE_NAME: ghcr.io/loculus-project/preprocessing-nextclade
 
 defaults:
   run:

.github/workflows/update-argocd-metadata.yml

@@ -40,7 +40,7 @@ jobs:
     - name: Checkout External Repository
       uses: actions/checkout@v4
       with:
-        repository: 'pathoplexus/argocd_metadata'
+        repository: 'loculus-project/argocd_metadata'
         token: ${{ secrets.ARGOCD_METADATA_PAT }}
 
     - name: Modify config.json

.github/workflows/website.yml

@@ -4,7 +4,7 @@ on:
   push:
 
 env:
-  DOCKER_IMAGE_NAME: ghcr.io/pathoplexus/website
+  DOCKER_IMAGE_NAME: ghcr.io/loculus-project/website
 
 defaults:
   run:

README.md

@@ -64,5 +64,5 @@ For testing we added multiple users to the realm. The users are:
 ## Contributing to Loculus
 
 Contributions are very welcome!
-Please see [`CONTRIBUTING.md`](https://github.com/pathoplexus/loculus/blob/main/CONTRIBUTING.md)
+Please see [`CONTRIBUTING.md`](https://github.com/loculus-project/loculus/blob/main/CONTRIBUTING.md)
 for more information or ping us in case you need help.

kubernetes/README.md

@@ -140,7 +140,7 @@ This will return a base64 encoded string similar to the one you can see above th
 
 Using Docker desktop as your container runtime won't work on ARM64 macOS. Instead, you will need to use `colima` to run an AMD64 VM which will host AMD64 docker containers.
 
-This will be quite slow due to QEMU emulation but it will work nonetheless (you may need to [adjust timeouts](https://github.com/pathoplexus/loculus/pull/583).
+This will be quite slow due to QEMU emulation but it will work nonetheless (you may need to [adjust timeouts](https://github.com/loculus-project/loculus/pull/583).
 
 First, install `colima`:
 

kubernetes/appset.yaml

@@ -9,7 +9,7 @@ spec:
   generators:
     - pullRequest:
         github:
-          owner: pathoplexus
+          owner: loculus-project
           labels:
             - preview
           repo: loculus
@@ -18,7 +18,7 @@ spec:
             secretName: github-access-token
         requeueAfterSeconds: 60
     - git:
-        repoURL: https://github.com/pathoplexus/argocd_metadata.git
+        repoURL: https://github.com/loculus-project/argocd_metadata.git
         revision: HEAD
         files:
         - path: "config.json"
@@ -33,7 +33,7 @@ spec:
       project: default
       source:
         path: 'kubernetes/loculus/'
-        repoURL: 'https://github.com/pathoplexus/loculus.git'
+        repoURL: 'https://github.com/loculus-project/loculus.git'
         targetRevision: '{{.branch}}'
         helm:
           parameters:

kubernetes/loculus/templates/loculus-deployment.yaml

@@ -22,7 +22,7 @@ spec:
       containers:
         {{- if not .Values.disableWebsite }}
         - name: website
-          image: "ghcr.io/pathoplexus/website:{{ $dockerTag }}"
+          image: "ghcr.io/loculus-project/website:{{ $dockerTag }}"
           imagePullPolicy: Always
           resources:
             requests:
@@ -51,7 +51,7 @@ spec:
         {{- end }}
         {{- if not .Values.disableBackend }}
         - name: backend
-          image: "ghcr.io/pathoplexus/backend:{{ $dockerTag }}"
+          image: "ghcr.io/loculus-project/backend:{{ $dockerTag }}"
           imagePullPolicy: Always
           livenessProbe:
             httpGet:

kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml

@@ -30,7 +30,7 @@ spec:
       containers:
         {{- range $key, $_ := $configFile.instances }}
         - name: preprocessing-{{ $key }}
-          image: ghcr.io/pathoplexus/preprocessing-dummy:{{ $dockerTag }}
+          image: ghcr.io/loculus-project/preprocessing-dummy:{{ $dockerTag }}
           imagePullPolicy: Always
           args:
             - "--watch"

website/.eslintrc.cjs

@@ -42,7 +42,7 @@ module.exports = {
     },
     {
       // Prettier is stubborn, need to accept its rules in case of conflict
-      // See https://github.com/pathoplexus/loculus/pull/283#issuecomment-1733872357
+      // See https://github.com/loculus-project/loculus/pull/283#issuecomment-1733872357
       files: ['*'],
       rules: {
         'react/self-closing-comp': 'off',

website/src/components/ConfirmationDialog.tsx

@@ -19,7 +19,7 @@ export const ConfirmationDialog: FC<ConfirmationDialogProps> = ({ dialogText, on
                     <button className='btn btn-error'>Cancel</button>
                 </form>
                 <form method='dialog'>
-                    <button className='btn pathoplexusGreen' onClick={onConfirmation}>
+                    <button className='btn loculusGreen' onClick={onConfirmation}>
                         Confirm
                     </button>
                 </form>

website/src/components/Navigation/SandwichMenu.tsx

@@ -56,7 +56,7 @@ export const SandwichMenu: FC<SandwichMenuProps> = ({ top, right, organism, know
 
                     <div className='mt-auto mb-10'>
                         <div className='flex justify-end items-center py-5'>
-                            <a href='https://github.com/pathoplexus'>
+                            <a href='https://github.com/loculus-project'>
                                 <img src='/github-mark.svg' className='w-8' alt='GitHub logo' />
                             </a>
                         </div>

website/src/hooks/useGroupOperations.ts

@@ -87,7 +87,7 @@ export const useGroupPageHooks = ({
 
 export const useGroupManagementClient = (clientConfig: ClientConfig) => {
     const zodios = useMemo(() => new Zodios(clientConfig.backendUrl, groupManagementApi), [clientConfig]);
-    const zodiosHooks = useMemo(() => new ZodiosHooks('pathoplexus', zodios), [zodios]);
+    const zodiosHooks = useMemo(() => new ZodiosHooks('loculus', zodios), [zodios]);
     return {
         zodios,
         zodiosHooks,

website/src/layouts/BaseLayout.astro

@@ -55,7 +55,7 @@ const { title } = Astro.props;
                     }
                 </div>
 
-                <a href='https://github.com/pathoplexus' class='h-full py-6'>
+                <a href='https://github.com/loculus-project' class='h-full py-6'>
                     <img src='/github-mark.svg' class='h-full object-scale-down' alt='github-icon' />
                 </a>
             </footer>