chore(docs): check formatting of docs in ci and do initial formatting

.github/workflows/docs-test.yml

@@ -31,3 +31,6 @@ jobs:
       - name: Check Build
         run: npm run build
         working-directory: ./docs
+      - name: Check Format
+        run: npm run check-format
+        working-directory: ./docs

docs/.prettierrc

@@ -13,6 +13,12 @@
       "options": {
         "parser": "astro"
       }
+    },
+    {
+      "files": ["*.md", "*.mdx"],
+      "options": {
+        "tabWidth": 2
+      }
     }
   ]
 }

docs/README.md

@@ -34,6 +34,8 @@ All commands are run from the root of the project, from a terminal:
 | :------------------------ | :----------------------------------------------- |
 | `npm install`             | Installs dependencies                            |
 | `npm run dev`             | Starts local dev server at `localhost:4321`      |
+| `npm run format`          | Formats your code using Prettier                 |
+| `npm run check-format`    | Checks if your code is formatted correctly       |
 | `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` |

docs/astro.config.mjs

@@ -70,8 +70,8 @@ export default defineConfig({
                             items: [
                                 'for-administrators/pipeline-concept',
                                 'for-administrators/existing-preprocessing-pipelines',
-                                'for-administrators/build-new-preprocessing-pipeline'
-                            ]
+                                'for-administrators/build-new-preprocessing-pipeline',
+                            ],
                         },
                         { label: 'Data use terms', link: '/for-administrators/data-use-terms/' },
                         { label: 'User administration', link: '/for-administrators/user-administration/' },

docs/package.json

@@ -9,7 +9,8 @@
         "build": "astro check && astro build",
         "preview": "astro preview",
         "astro": "astro",
-        "format": "prettier --ignore-path \"../.gitignore\" --write \"./**/*.{ts,tsx,json,astro,md,mdx,mjs,cjs}\""
+        "check-format": "prettier --ignore-path \"../.gitignore\" --ignore-path .gitignore  --check \"./**/*.{ts,tsx,json,astro,md,mdx,mjs,cjs}\"",
+        "format": "prettier --ignore-path \"../.gitignore\" --ignore-path .gitignore --write \"./**/*.{ts,tsx,json,astro,md,mdx,mjs,cjs}\""
     },
     "dependencies": {
         "@astrojs/check": "^0.9.4",

docs/src/components/MarkdownRenderer.astro

@@ -9,10 +9,7 @@ import rehypeStringify from 'rehype-stringify';
 
 const { content } = Astro.props;
 
-const html = String(await unified()
-    .use(remarkParse)
-    .use(remarkRehype)
-    .use(rehypeStringify)
-    .process(content));
+const html = String(await unified().use(remarkParse).use(remarkRehype).use(rehypeStringify).process(content));
 ---
-<div set:html={html}></div>
+
+<div set:html={html} />

docs/src/components/SchemaDocs.astro

@@ -4,7 +4,12 @@
  * Properties in the schema can be assigned to groups by adding a new "groups": ["group1", "group2"] key to them.
  * This way, you can split schema definition into semantic groups.
  */
-import { type JSONSchema7, type JSONSchema7Definition, type JSONSchema7TypeName, type JSONSchema7Type } from 'json-schema';
+import {
+    type JSONSchema7,
+    type JSONSchema7Definition,
+    type JSONSchema7TypeName,
+    type JSONSchema7Type,
+} from 'json-schema';
 import MarkdownRenderer from './MarkdownRenderer.astro';
 import rawSchema from '../values.schema.json';
 
@@ -26,24 +31,24 @@ function capitalizeFirst(str: string) {
  */
 function typeToString(
     type: JSONSchema7TypeName | JSONSchema7TypeName[] | undefined,
-    enumvals: JSONSchema7Type[] | undefined
+    enumvals: JSONSchema7Type[] | undefined,
 ) {
-    if (type === undefined) return "";
+    if (type === undefined) return '';
     if (Array.isArray(type)) {
-        return type.map(t => capitalizeFirst(String(t))).join(", ")
+        return type.map((t) => capitalizeFirst(String(t))).join(', ');
     }
-    if (type === "string" && enumvals !== undefined) {
-        return enumvals?.map(enumval => String(enumval)).join(", ")
+    if (type === 'string' && enumvals !== undefined) {
+        return enumvals?.map((enumval) => String(enumval)).join(', ');
     }
     return capitalizeFirst(String(type));
 }
 
 /** A row in the table. */
 interface Row {
-    key: string,
-    type?: string,
-    default?: string,
-    description?: string
+    key: string;
+    type?: string;
+    default?: string;
+    description?: string;
 }
 
 const rows: Row[] = [];
@@ -55,44 +60,40 @@ const rows: Row[] = [];
  * @param definition The definition of the property currently observed.
  */
 function addSelfAndChildren(prefix: string, key: string, definition: JSONSchema7Definition) {
-    if (
-        typeof definition === 'object' &&
-        definition !== null
-    ) {
+    if (typeof definition === 'object' && definition !== null) {
         if ('placeholder' in definition) {
             key = `<${definition.placeholder}>`;
         }
         if ('docsIncludePrefix' in definition && definition.docsIncludePrefix === false) {
-            prefix = "";
+            prefix = '';
         }
-        if (
-            'groups' in definition &&
-            Array.isArray(definition.groups) &&
-            definition.groups.includes(group)
-        ) {
-            var def = definition.default !== undefined ? String(definition.default) : "";
-            if (definition.type === "string" && def !== "") {
-                def = `"${def}"`
+        if ('groups' in definition && Array.isArray(definition.groups) && definition.groups.includes(group)) {
+            var def = definition.default !== undefined ? String(definition.default) : '';
+            if (definition.type === 'string' && def !== '') {
+                def = `"${def}"`;
             }
             rows.push({
                 key: `${prefix}${key}`,
                 type: typeToString(definition.type, definition.enum),
                 default: def,
-                description: definition.description
-            })
+                description: definition.description,
+            });
         }
         if ('properties' in definition && definition.properties) {
             Object.entries(definition.properties).forEach(([k, d]) => addSelfAndChildren(`${prefix}${key}.`, k, d));
         }
         if ('patternProperties' in definition && definition.patternProperties) {
-            Object.entries(definition.patternProperties).forEach(([k, d]) => addSelfAndChildren(`${prefix}${key}.`, k, d));
+            Object.entries(definition.patternProperties).forEach(([k, d]) =>
+                addSelfAndChildren(`${prefix}${key}.`, k, d),
+            );
         }
         if ('items' in definition && definition.items !== undefined && typeof definition.items === 'object') {
             const items = definition.items;
-            if ('length' in items) { // filter out arrays
+            if ('length' in items) {
+                // filter out arrays
                 return;
             }
-            addSelfAndChildren(`${prefix}${key}.`, "[]", items)
+            addSelfAndChildren(`${prefix}${key}.`, '[]', items);
         }
     }
 }
@@ -101,7 +102,7 @@ if (schema.definitions) {
     Object.entries(schema.definitions).forEach(([_, definition]) => {
         if (typeof definition === 'object' && definition.properties) {
             Object.entries(definition.properties).forEach(([key, definition]) => {
-                addSelfAndChildren("", key, definition);
+                addSelfAndChildren('', key, definition);
             });
         }
     });
@@ -110,10 +111,9 @@ if (schema.definitions) {
 // start of recursing with the top level properties in the schema.
 if (schema.properties) {
     Object.entries(schema.properties).forEach(([key, definition]) => {
-        addSelfAndChildren("", key, definition);
+        addSelfAndChildren('', key, definition);
     });
 }
-
 ---
 
 <div class='overflow-x-scroll'>
@@ -128,12 +128,16 @@ if (schema.properties) {
         </thead>
         <tbody>
             {
-                rows.map(row => (
+                rows.map((row) => (
                     <tr>
-                        <td><code>{row.key}</code></td>
+                        <td>
+                            <code>{row.key}</code>
+                        </td>
                         <td>{row.type}</td>
                         <td>{row.default}</td>
-                        <td><MarkdownRenderer content={row.description} /></td>
+                        <td>
+                            <MarkdownRenderer content={row.description} />
+                        </td>
                     </tr>
                 ))
             }

docs/src/content/docs/for-administrators/data-use-terms.mdx

@@ -5,7 +5,11 @@ description: What's the data use terms concept of Loculus and how to configure i
 
 import { Aside } from '@astrojs/starlight/components';
 
-<Aside type="caution">The data use terms currently hardcode textual descriptions and behaviour designed around the Pathoplexus database. You can disable the data use terms entirely, as below. If you require custom data use terms handling please feel free to reach out to us by raising a Github issue.</Aside>
+<Aside type='caution'>
+  The data use terms currently hardcode textual descriptions and behaviour designed around the Pathoplexus database. You
+  can disable the data use terms entirely, as below. If you require custom data use terms handling please feel free to
+  reach out to us by raising a Github issue.
+</Aside>
 
 Loculus comes with built-in handling of data use terms for submitted data, which means that data can either be _open_ or _restricted_. You can define, what restricted means yourself. Users can submit data as restricted, but they have to give a date at which point the sequences become open, this date can at most be one year from the submission date.
 

docs/src/content/docs/for-administrators/existing-preprocessing-pipelines.md

@@ -16,8 +16,8 @@ Given a nextclade dataset this pipeline uses [nextclade run](https://docs.nextst
 
 ```yaml
 preprocessing:
-    - configFile:
-          nextclade_dataset_name: nextstrain/mpox/all-clades
+  - configFile:
+      nextclade_dataset_name: nextstrain/mpox/all-clades
 ```
 
 Additionally the pipeline performs checks on the metadata fields. The checks are defined by custom preprocessing functions in the `values.yaml` file. These checks can be applied to and customized for other metadata fields, see [Preprocessing Checks](https://github.com/loculus-project/loculus/blob/main/preprocessing/nextclade/README.md#preprocessing-checks) for more info.

docs/src/content/docs/for-administrators/pipeline-concept.md

@@ -25,4 +25,4 @@ While the exact functionality depends on the specific pipeline, generally a pipe
 
 As the preprocessing logic might change over time, preprocessing pipelines are versioned (You specify the pipeline version under `<organismConfig>.preprocessing.version`).
 The backend keeps track of which sequences have successfully been processed with which pipeline version.
-Once all data for an organism has successfully been processed with a new version, that version will also automatically be served to users.
+Once all data for an organism has successfully been processed with a new version, that version will also automatically be served to users.

docs/src/content/docs/for-administrators/sequence-reporting.md

@@ -12,7 +12,7 @@ sequenceFlagging:
   github:
     organization: pathoplexus
     repository: curation_reports
-    issueTemplate: sequence-metadata-issue.md  # (optional)
+    issueTemplate: sequence-metadata-issue.md # (optional)
 ```
 
 Sequence reporting is done through GitHub issues.

docs/src/content/docs/for-administrators/setup-with-k3d-and-nginx.mdx

@@ -98,62 +98,62 @@ runDevelopmentMainDatabase: true
 runDevelopmentKeycloakDatabase: true
 
 website:
-    runtimeConfig:
-        public:
-            backendUrl: 'https://api.<your domain>/backend'
-            lapisUrlTemplate: 'https://api.<your domain>/%organism%'
-            keycloakUrl: 'https://auth.<your domain>'
+  runtimeConfig:
+    public:
+      backendUrl: 'https://api.<your domain>/backend'
+      lapisUrlTemplate: 'https://api.<your domain>/%organism%'
+      keycloakUrl: 'https://auth.<your domain>'
 
 auth:
-    verifyEmail: false
-    resetPasswordAllowed: false
-    registrationAllowed: true
-    smtp: null
-    identityProviders: null
+  verifyEmail: false
+  resetPasswordAllowed: false
+  registrationAllowed: true
+  smtp: null
+  identityProviders: null
 
 disableIngest: true
 disableEnaSubmission: true
 
 seqSets:
-    enabled: false
+  enabled: false
 
 secrets:
-    keycloak-admin:
-        type: raw
-        data:
-            initialAdminPassword: '<your initial admin password>'
+  keycloak-admin:
+    type: raw
+    data:
+      initialAdminPassword: '<your initial admin password>'
 
 organisms:
-    angelovirus:
-        schema:
-            organismName: 'Angelovirus'
-            metadata:
-                - name: country
-                  type: string
-                  initiallyVisible: true
-                - name: city
-                  type: string
-                  initiallyVisible: true
-            website:
-                tableColumns:
-                    - country
-                    - city
-                defaultOrder: descending
-                defaultOrderBy: country
-        preprocessing:
-            - version: 1
-              image: ghcr.io/loculus-project/preprocessing-nextclade
-              args:
-                  - 'prepro'
-              configFile:
-                  log_level: DEBUG
-                  genes: []
-                  batch_size: 100
-        referenceGenomes:
-            nucleotideSequences:
-                - name: 'main'
-                  sequence: 'NNN' # We are not performing alignment here, so this sequence doesn't matter
-            genes: []
+  angelovirus:
+    schema:
+      organismName: 'Angelovirus'
+      metadata:
+        - name: country
+          type: string
+          initiallyVisible: true
+        - name: city
+          type: string
+          initiallyVisible: true
+      website:
+        tableColumns:
+          - country
+          - city
+        defaultOrder: descending
+        defaultOrderBy: country
+    preprocessing:
+      - version: 1
+        image: ghcr.io/loculus-project/preprocessing-nextclade
+        args:
+          - 'prepro'
+        configFile:
+          log_level: DEBUG
+          genes: []
+          batch_size: 100
+    referenceGenomes:
+      nucleotideSequences:
+        - name: 'main'
+          sequence: 'NNN' # We are not performing alignment here, so this sequence doesn't matter
+      genes: []
 ```
 
 ## Step 4: Install and deploy
@@ -300,20 +300,20 @@ Then, adapt `my-values.yaml` and add under the `secrets` key:
 
 ```yaml
 secrets:
-    database:
-        type: raw
-        data:
-            url: 'jdbc:postgresql://<Loculus database host>:<Loculus database port>/<Loculus database name>'
-            username: '<Loculus database user>'
-            password: '<Loculus database password>'
-    keycloak-database:
-        type: raw
-        data:
-            addr: '<Keycloak database host>'
-            port: '<Keycloak database port>'
-            database: '<Keycloak database name>'
-            username: '<Keycloak database user>'
-            password: '<Keycloak database password>'
+  database:
+    type: raw
+    data:
+      url: 'jdbc:postgresql://<Loculus database host>:<Loculus database port>/<Loculus database name>'
+      username: '<Loculus database user>'
+      password: '<Loculus database password>'
+  keycloak-database:
+    type: raw
+    data:
+      addr: '<Keycloak database host>'
+      port: '<Keycloak database port>'
+      database: '<Keycloak database name>'
+      username: '<Keycloak database user>'
+      password: '<Keycloak database password>'
 ```
 
 To reinstall Loculus, execute: