Fix Vale action configuration for GitHub PR reviews

.github/styles/config/vocabularies/Docs/accept.txt

@@ -1 +1,41 @@
 Astro
+nf-core
+Nextflow
+Seqera
+SeqeraLabs
+Bytesize
+Conda
+Mamba
+Bioconda
+Singularity
+Apptainer
+Docker
+GitHub
+GitLab
+Bitbucket
+AWS
+Azure
+GCP
+S3
+Kubernetes
+Slurm
+PBS
+LSF
+SGE
+TORQUE
+HTCondor
+Podman
+Charliecloud
+Shifter
+Spack
+OpenEBench
+MultiQC
+FastQC
+nf-test
+DSL2
+Groovy
+CWL
+WDL
+Snakemake
+Prefect
+Cromwell

.github/workflows/linting.yml

@@ -5,26 +5,36 @@ on:
       - main
   pull_request:
 
+permissions:
+  contents: read
+  pull-requests: write
+  checks: write
+
 jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
-        with:
-          node-version: 20
       - run: npm install --only=dev
+      - name: Install custom mdx2vast for MDX directive vale support
+        run: npm install -g https://github.com/edmundmiller/mdx2vast.git
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
   vale:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-      - name: Install Vale
-        run: |
-          wget https://github.com/errata-ai/vale/releases/download/v3.0.5/vale_3.0.5_Linux_64-bit.tar.gz -O vale.tar.gz
-          tar -xvzf vale.tar.gz vale
-          rm vale.tar.gz
-      - name: Spell check
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
+      - name: Install custom mdx2vast for MDX directive support
+        run: npm install -g https://github.com/edmundmiller/mdx2vast.git
+      - name: Verify Vale setup
         run: |
-          ./vale sync
-          ./vale ${{inputs.DOC_SRC}}
+          echo "Vale config:" && cat .vale.ini
+          echo "mdx2vast installed:" && which mdx2vast
+      - uses: errata-ai/[email protected]
+        with:
+          files: sites/main-site/src/content,sites/docs/src/content,sites/configs/src/content,sites/modules-subworkflows/src/content,sites/pipelines/src/content
+          reporter: github-pr-check
+          fail_on_error: true
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

.pre-commit-config.yaml

@@ -9,3 +9,12 @@ repos:
           - [email protected]
           - [email protected]
         files: \.(astro|svelte|mdx|md|yml|yaml)$
+  - repo: https://github.com/errata-ai/vale
+    rev: v3.7.1
+    hooks:
+      - id: vale
+        name: vale sync
+        pass_filenames: false
+        args: [sync]
+      - id: vale
+        args: [--output=line, --minAlertLevel=error]

.vale.ini

@@ -1,20 +1,87 @@
 StylesPath = .github/styles
-MinAlertLevel = suggestion
+MinAlertLevel = warning
 
-Packages = https://github.com/nf-core/vale/releases/latest/download/nf-core.zip
+Packages = MDX, https://github.com/nf-core/vale/releases/latest/download/nf-core.zip
 Vocab = Docs
 
-[*.md]
+# Global settings for all Markdown and MDX files
+[*.{md,mdx}]
 BasedOnStyles = nf-core, Vale
 Vale.Spelling = NO
 
-[src/content/events/**]
+# Blog posts - apply standard rules with relaxed personal pronouns
+[sites/main-site/src/content/blog/**/*.{md,mdx}]
+BasedOnStyles = nf-core, Vale
+Vale.Spelling = NO
 nf-core.We = NO
-nf-core.SeqeraLabs = NO
 
-[src/content/events/2024]
-nf-core.SeqeraLabs = YES
+# Documentation - stricter rules for formal documentation
+[sites/docs/src/content/**/*.{md,mdx}]
+BasedOnStyles = nf-core, Vale
+Vale.Spelling = NO
+
+
+# Component and pipeline pages
+[sites/modules-subworkflows/src/content/**/*.{md,mdx}]
+BasedOnStyles = nf-core, Vale
+Vale.Spelling = NO
+
+[sites/pipelines/src/content/**/*.{md,mdx}]
+BasedOnStyles = nf-core, Vale
+Vale.Spelling = NO
 
-[src/content/events/*/bytesize_*.md]
+# Config pages
+[sites/configs/src/content/**/*.{md,mdx}]
 BasedOnStyles = nf-core, Vale
 Vale.Spelling = NO
+
+# Ignore API reference documentation (auto-generated) - must be at end
+[sites/docs/src/content/api_reference/**/*.md]
+BasedOnStyles =
+
+[sites/docs/src/content/api_reference/**/*.mdx]
+BasedOnStyles =
+
+# Ignore events from previous years only (2024 and before) - must be at end
+[sites/main-site/src/content/events/2018/**/*.md]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2019/**/*.md]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2020/**/*.md]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2021/**/*.md]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2022/**/*.md]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2023/**/*.md]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2024/**/*.md]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2018/**/*.mdx]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2019/**/*.mdx]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2020/**/*.mdx]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2021/**/*.mdx]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2022/**/*.mdx]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2023/**/*.mdx]
+BasedOnStyles =
+
+[sites/main-site/src/content/events/2024/**/*.mdx]
+BasedOnStyles =
+

.vscode/extensions.json

@@ -0,0 +1,28 @@
+{
+  "recommendations": [
+    // Documentation and linting
+    "errata-ai.vale-server",
+    "davidanson.vscode-markdownlint",
+    "streetsidesoftware.code-spell-checker",
+
+    // Formatting and Prettier
+    "esbenp.prettier-vscode",
+
+    // Astro and web development
+    "astro-build.astro-vscode",
+    "bradlc.vscode-tailwindcss",
+
+    // YAML and configuration files
+    "redhat.vscode-yaml",
+
+    // Git and version control
+    "eamodio.gitlens",
+
+    // Commitizen support
+    "commitizen.git-conventional-commits",
+
+    // Link checking (if available)
+    "tchayen.markdown-links"
+  ],
+  "unwantedRecommendations": []
+}

.vscode/settings.json

@@ -1,5 +1,48 @@
 {
   "markdown.styles": [
     "public/vscode_markdown.css"
-  ]
+  ],
+
+  "// Documentation linting and formatting": "",
+  "vale.valeCLI.config": ".vale.ini",
+  "vale.valeCLI.path": "vale",
+  "vale.core.useCLI": true,
+
+  "[markdown]": {
+    "editor.defaultFormatter": "esbenp.prettier-vscode",
+    "editor.formatOnSave": true,
+    "editor.rulers": [120],
+    "editor.wordWrap": "wordWrapColumn",
+    "editor.wordWrapColumn": 120
+  },
+
+  "// MDX settings": "",
+  "[mdx]": {
+    "editor.defaultFormatter": "esbenp.prettier-vscode",
+    "editor.formatOnSave": true,
+    "editor.rulers": [120],
+    "editor.wordWrap": "wordWrapColumn",
+    "editor.wordWrapColumn": 120
+  },
+
+  "// YAML settings": "",
+  "[yaml]": {
+    "editor.defaultFormatter": "esbenp.prettier-vscode",
+    "editor.formatOnSave": true,
+    "editor.insertSpaces": true,
+    "editor.tabSize": 2
+  },
+
+  "// Astro settings": "",
+  "[astro]": {
+    "editor.defaultFormatter": "esbenp.prettier-vscode",
+    "editor.formatOnSave": true
+  },
+
+  "// File explorer": "",
+  "files.exclude": {
+    "**/node_modules": true,
+    "**/dist": true,
+    "**/.astro": true
+  }
 }