Merge branch 'main' into add_ena_slack_notifications

.github/workflows/ingest-tests.yaml

@@ -0,0 +1,36 @@
+name: ingest-tests
+on:
+  # test
+  pull_request:
+    paths:
+      - "ingest/**"
+      - ".github/workflows/ingest-tests.yml"
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+concurrency:
+  group: ci-${{ github.ref == 'refs/heads/main' && github.run_id || github.ref }}-ingest-tests
+  cancel-in-progress: true
+jobs:
+  unitTests:
+    name: Unit Tests
+    runs-on: codebuild-loculus-ci-${{ github.run_id }}-${{ github.run_attempt }}
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ingest/environment.yml
+          micromamba-version: 'latest'
+          init-shell: >-
+            bash powershell
+          cache-environment: true
+          post-cleanup: 'all'
+      - name: Run tests
+        run: |
+          micromamba activate loculus-ingest
+          pytest tests/
+        shell: micromamba-shell {0}
+        working-directory: ingest

backend/build.gradle

@@ -4,8 +4,8 @@ import org.gradle.api.tasks.testing.logging.TestLogEvent
 plugins {
     id 'org.springframework.boot' version '3.3.2'
     id 'io.spring.dependency-management' version '1.1.6'
-    id 'org.jetbrains.kotlin.jvm' version '2.0.0'
-    id 'org.jetbrains.kotlin.plugin.spring' version '2.0.0'
+    id 'org.jetbrains.kotlin.jvm' version '2.0.10'
+    id 'org.jetbrains.kotlin.plugin.spring' version '2.0.10'
     id 'org.jlleitschuh.gradle.ktlint' version '12.1.1'
     id 'org.springdoc.openapi-gradle-plugin' version '1.9.0'
 }
@@ -47,7 +47,7 @@ dependencies {
     implementation "org.springframework.boot:spring-boot-starter-oauth2-resource-server"
     implementation "org.springframework.boot:spring-boot-starter-security"
 
-    implementation 'org.apache.commons:commons-compress:1.26.2'
+    implementation 'org.apache.commons:commons-compress:1.27.0'
     implementation 'com.github.luben:zstd-jni:1.5.6-4'
     implementation 'org.tukaani:xz:1.10'
 

docs/.prettierrc

@@ -0,0 +1,18 @@
+{
+  "printWidth": 120,
+  "tabWidth": 4,
+  "trailingComma": "all",
+  "semi": true,
+  "jsxSingleQuote": true,
+  "singleQuote": true,
+  "quoteProps": "consistent",
+  "plugins": ["prettier-plugin-astro", "prettier-plugin-tailwindcss"],
+  "overrides": [
+    {
+      "files": "*.astro",
+      "options": {
+        "parser": "astro"
+      }
+    }
+  ]
+}

docs/.vite/deps/_metadata.json

@@ -1,8 +1,8 @@
 {
-  "hash": "c1e8de51",
-  "configHash": "0c82321a",
-  "lockfileHash": "25f1fc72",
-  "browserHash": "cf2b5ff5",
-  "optimized": {},
-  "chunks": {}
+    "hash": "c1e8de51",
+    "configHash": "0c82321a",
+    "lockfileHash": "25f1fc72",
+    "browserHash": "cf2b5ff5",
+    "optimized": {},
+    "chunks": {}
 }

docs/.vite/deps/package.json

@@ -1,3 +1,3 @@
 {
-  "type": "module"
+    "type": "module"
 }

docs/.vscode/extensions.json

@@ -1,4 +1,4 @@
 {
-  "recommendations": ["astro-build.astro-vscode"],
-  "unwantedRecommendations": []
+    "recommendations": ["astro-build.astro-vscode"],
+    "unwantedRecommendations": []
 }

docs/.vscode/launch.json

@@ -1,11 +1,11 @@
 {
-  "version": "0.2.0",
-  "configurations": [
-    {
-      "command": "./node_modules/.bin/astro dev",
-      "name": "Development server",
-      "request": "launch",
-      "type": "node-terminal"
-    }
-  ]
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "command": "./node_modules/.bin/astro dev",
+            "name": "Development server",
+            "request": "launch",
+            "type": "node-terminal"
+        }
+    ]
 }

docs/README.md

@@ -39,6 +39,6 @@ All commands are run from the root of the project, from a terminal:
 | `npm run astro ...`       | Run CLI commands like `astro add`, `astro check` |
 | `npm run astro -- --help` | Get help using the Astro CLI                     |
 
-##  More information.
+## More information.
 
 Check out [Starlight’s docs](https://starlight.astro.build/), read [the Astro documentation](https://docs.astro.build).

docs/astro.config.mjs

@@ -1,33 +1,44 @@
-import { defineConfig } from "astro/config";
-import starlight from "@astrojs/starlight";
+import { defineConfig } from 'astro/config';
+import starlight from '@astrojs/starlight';
+import tailwind from '@astrojs/tailwind';
 
 // https://astro.build/config
 export default defineConfig({
-  base: "/loculus/",
-  integrations: [
-    starlight({
-      title: "Loculus",
-      editLink: {
-        baseUrl: "https://github.com/loculus-project/loculus/edit/main/docs/",
-      },
-
-      social: {
-        github: "https://github.com/loculus-project/loculus",
-      },
-      sidebar: [
-        {
-          label: "Guides",
-          items: [
-            // Each item here is one entry in the navigation menu.
-            { label: "Getting started", link: "/guides/getting-started/" },
-            { label: "User administration", link: "/guides/user-administration/" },
-          ],
-        },
-        {
-          label: "Reference",
-          autogenerate: { directory: "reference" },
-        },
-      ],
-    }),
-  ],
+    base: '/loculus/',
+    integrations: [
+        starlight({
+            title: 'Loculus',
+            editLink: {
+                baseUrl: 'https://github.com/loculus-project/loculus/edit/main/docs/',
+            },
+            customCss: ['./src/styles/custom.css'],
+            social: {
+                github: 'https://github.com/loculus-project/loculus',
+            },
+            sidebar: [
+                {
+                    label: 'Introduction',
+                    items: [
+                        { label: 'What is Loculus?', link: '/introduction/what-is-loculus/' },
+                        { label: 'Current state and roadmap', link: '/introduction/current-state-and-roadmap/' },
+                        { label: 'Glossary', link: '/introduction/glossary/' },
+                        { label: 'System overview', link: '/introduction/system-overview/' },
+                    ],
+                },
+                {
+                    label: 'For administrators',
+                    items: [
+                        { label: 'Getting started', link: '/for-administrators/getting-started/' },
+                        { label: 'Setup with Kubernetes', link: '/for-administrators/setup-with-kubernetes/' },
+                        { label: 'User administration', link: '/for-administrators/user-administration/' },
+                    ],
+                },
+                {
+                    label: 'Reference',
+                    autogenerate: { directory: 'reference' },
+                },
+            ],
+        }),
+        tailwind(),
+    ],
 });