sync with nf-core website in prep for v2 release

Author: keiran-rowell-unsw

.cache.tar.xz

@@ -0,0 +1,18 @@
+FROM mcr.microsoft.com/devcontainers/javascript-node:4-20-bookworm@sha256:1f16317eacca7950213a174750ad513b69e91984b04cc1b61d460bc8780108f7
+
+# Set working directory
+WORKDIR /workspace
+
+# Copy root package files
+COPY package.json package-lock.json* ./
+
+# Copy only package.json files from each workspace
+COPY sites/configs/package.json ./sites/configs/package.json
+COPY sites/docs/package.json ./sites/docs/package.json
+COPY sites/main-site/package.json ./sites/main-site/package.json
+COPY sites/modules-subworkflows/package.json ./sites/modules-subworkflows/package.json
+COPY sites/pipeline-results/package.json ./sites/pipeline-results/package.json
+COPY sites/pipelines/package.json ./sites/pipelines/package.json
+
+# Install dependencies
+RUN npm install --workspaces

.devcontainer/Dockerfile

@@ -0,0 +1,22 @@
+{
+  "name": "nf-core.astro",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": ".."
+  },
+  "portsAttributes": {
+    "4321": {
+      "label": "Astro Dev Server",
+      "onAutoForward": "openPreview"
+    }
+  },
+  "customizations": {
+    "vscode": {
+      "extensions": ["astro-build.astro-vscode", "editorconfig.editorconfig", "esbenp.prettier-vscode"]
+    }
+  },
+  "waitFor": "onCreateCommand",
+  "postAttachCommand": {
+    "server": "npm run dev --workspace sites/main-site -- --host"
+  }
+}

.devcontainer/devcontainer.json

@@ -1,2 +1,4 @@
 src/content/docs @nf-core/docs
 src/content/tutorials @nf-core/training @nf-core/outreach
+
+sites/main-site/src/content/about/governance.mdx @ewels @christopher-hakkaart @FranBonath @mribeirodantas @FriederikeHanssen @jfy133 @maxulysse

.github/CODEOWNERS

@@ -13,7 +13,7 @@ Hi there! Many thanks for taking an interest in improving the nf-core website.
 ## Instructions to add your institution to the list of contributors
 
 1. Fork this repo
-2. Add your institute details and your name to the [contributors.yaml](../src/config/contributors.yaml)
+2. Add your institute details and your name to the [contributors.yaml](../sites/main-site/src/config/contributors.yaml)
 
 Here's the desired format
 
@@ -61,7 +61,14 @@ If you're not used to this workflow with git, you can start with some [basic doc
 
 When you create a pull request with changes, Github Actions will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
-For now, the only test is for Markdown syntax, using the `markdownlint` package.
+For now, the main test is for syntax formatting using prettier.
+We use pre-commit to ensure that your code is formatted correctly before submitting your pull request. To automatically check your code before commiting, install [prek](https://prek.j178.dev/installation/) (comes installed as a dev dependency) and the pre-commit hooks defined in `pre-commit.config.yaml`:
+
+```
+prek install --install-hooks
+```
+
+You can manually run the tests using `prek run --all-files` to run all tests.
 
 ## Getting help
 

.github/CONTRIBUTING.md

@@ -3,6 +3,6 @@ contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join
     about: Please join the nf-core community here
-  - name: 'Slack #website channel'
+  - name: "Slack #website channel"
     url: https://nfcore.slack.com/channels/website
     about: Discussion about the nf-core website

.github/ISSUE_TEMPLATE/config.yml

@@ -1,15 +1,41 @@
 {
-    "$schema": "https://docs.renovatebot.com/renovate-schema.json",
-    "extends": ["github>nf-core/ops//.github/renovate/default.json5", "config:recommended", "schedule:monthly"],
-    "npm": {
-        "enabled": false,
+    $schema: "https://docs.renovatebot.com/renovate-schema.json",
+    extends: [
+        "github>nf-core/ops//.github/renovate/default.json5",
+        "config:recommended",
+        "schedule:monthly",
+    ],
+    npm: {
+        enabled: false,
     },
-    "customManagers": [
+    // Override :automergeBranch from default.json5 to use PR-based auto-merge
+    // This respects branch protection rules that require PRs
+    platformAutomerge: true,
+    automergeType: "pr",
+    automergeStrategy: "rebase",
+    packageRules: [
+        {
+            matchManagers: ["custom.regex"],
+            matchFileNames: [".pre-commit-config.yaml"],
+            groupName: "pre-commit npm dependencies",
+            groupSlug: "pre-commit-npm",
+        },
+    ],
+    customManagers: [
+        {
+            customType: "regex",
+            managerFilePatterns: ["/^linting\\.yml$/"],
+            matchStrings: [
+                "https://github.com/(?<depName>.*)/releases/download/(?<currentValue>.*)/.*.tar.gz",
+            ],
+            datasourceTemplate: "github-release-attachments",
+        },
         {
-            "customType": "regex",
-            "fileMatch": ["^linting\\.yml$"],
-            "matchStrings": ["https://github.com/(?<depName>.*)/releases/download/(?<currentValue>.*)/.*.tar.gz"],
-            "datasourceTemplate": "github-release-attachments"
-        }
+            customType: "regex",
+            managerFilePatterns: ["/.pre-commit-config.yaml$/"],
+            matchStrings: ["- (?<depName>[^@\\s]+)@(?<currentValue>[^\\s#]+)"],
+            datasourceTemplate: "npm",
+            versioningTemplate: "npm",
+        },
     ],
 }