add lychee to check links in docs (#181)

* add `link_checker.yml`

* check links

* update actions

* fix links

* update action

* update mdbook.yml

Author: rvhonorato

.github/workflows/ci.yml

@@ -45,14 +45,20 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
 
-      - name: Install mdBook
-        run: |
-          curl --proto '=https' --tlsv1.2 https://sh.rustup.rs -sSf -y | sh
-          rustup update
-          cargo install --version 0.5.2 mdbook
+      - name: Setup mdBook
+        uses: peaceiris/actions-mdbook@v2
+        with:
+          mdbook-version: "0.5.2"
+          # mdbook-version: 'latest'
 
       - name: Build docs
-        run: cd docs && mdbook build
+        run: mdbook build docs
+
+      - name: check links
+        uses: lycheeverse/lychee-action@v2
+        with:
+          args: docs/book/*.html --max-retries 1 --root-dir docs/src
+          fail: true
 
   coverage:
     runs-on: ubuntu-latest

.github/workflows/mdbook.yml

@@ -3,7 +3,7 @@ name: deploy mdBook site
 on:
   # Runs on pushes targeting the default branch
   push:
-    branches: main
+    branches: [main]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch: ~
@@ -28,16 +28,20 @@ jobs:
       MDBOOK_VERSION: 0.5.2
     steps:
       - uses: actions/checkout@v4
-      - name: Install mdBook
-        run: |
-          curl --proto '=https' --tlsv1.2 https://sh.rustup.rs -sSf -y | sh
-          rustup update
-          cargo install --version ${MDBOOK_VERSION} mdbook
+
+      - name: Setup mdBook
+        uses: peaceiris/actions-mdbook@v2
+        with:
+          mdbook-version: "0.5.2"
+          # mdbook-version: 'latest'
+
       - name: Setup Pages
         id: pages
         uses: actions/configure-pages@v4
+
       - name: Build with mdBook
         run: mdbook build docs
+
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
         with:
@@ -48,8 +52,11 @@ jobs:
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
+
     runs-on: ubuntu-latest
+
     needs: build
+
     steps:
       - name: Deploy to GitHub Pages
         id: deployment

docs/src/home.md

@@ -86,7 +86,7 @@ Results are organized by scenario and target, making it easy to compare performa
 4. **List your input files** in the required format
 5. **Run the benchmark** and analyze results
 
-See the [Setting Up a Benchmark](/setting-up-bm5) and [Writing a Benchmark YAML File](/usage#step-3-write-the-benchmark-configuration) sections for detailed instructions.
+See the [Setting Up a Benchmark](./setting-up-bm5.md) and [Writing a Benchmark YAML File](./usage.md#step-3-write-the-benchmark-configuration) sections for detailed instructions.
 
 ## Getting Help
 

docs/src/installation.md

@@ -12,7 +12,7 @@ The `haddock-runner` is designed for researchers, developers, and advanced users
 
 If you are new to HADDOCK, we recommend:
 
-- Completing the basic [HADDOCK3 tutorials](/education/HADDOCK3/index.md)
+- Completing the basic [HADDOCK3 tutorials](https://www.bonvinlab.org/education/HADDOCK3)
 - Familiarizing yourself with HADDOCK3 workflows and configuration
 
 For single target docking or small-scale experiments, consider using:
@@ -81,7 +81,7 @@ Available platforms will include:
 - `x86_64-apple-darwin` (macOS Intel)
 - `aarch64-apple-darwin` (macOS Apple Silicon)
 
-> **Note**: Pre-built binaries are coming soon. For now, please use Method 1 (crates.io) or see the [Development](/development) section for building from source.
+> **Note**: Pre-built binaries are coming soon. For now, please use Method 1 (crates.io) or see the [Development](./development.md) section for building from source.
 
 ## Post-Installation Setup
 
@@ -138,13 +138,12 @@ If you encounter installation issues:
 
 - Check the [GitHub Issues](https://github.com/haddocking/haddock-runner/issues) for known problems
 - Consult the [HADDOCK3 documentation](https://github.com/haddocking/haddock3) for HADDOCK-specific requirements
-- Contact the development team via the support channels mentioned in the [Getting Help](/getting-help) section
 
 ## Next Steps
 
 Now that you have `haddock-runner` installed, you're ready to:
 
-1. **Set up your first benchmark** - See [Setting Up a Benchmark](/setting-up-bm5)
-2. **Write a configuration file** - See [Writing a Benchmark YAML File](/usage#step-3-write-the-benchmark-configuration)
-3. **Prepare your input files** - See [Writing an Input List File](/usage#step-2-create-the-input-list-file)
-4. **Run your benchmark** - See [Running Haddock Runner](/usage#step-4-run-the-benchmark)
+1. **Set up your first benchmark** - See [Setting Up a Benchmark](./setting-up-bm5.md)
+2. **Write a configuration file** - See [Writing a Benchmark YAML File](./usage.md#step-3-write-the-benchmark-configuration)
+3. **Prepare your input files** - See [Writing an Input List File](./usage.md#step-2-create-the-input-list-file)
+4. **Run your benchmark** - See [Running Haddock Runner](./usage.md#step-4-run-the-benchmark)

docs/src/setting-up-bm5.md

@@ -6,7 +6,7 @@ This guide provides comprehensive, up-to-date instructions for setting up and ru
 
 Before starting, ensure you have:
 
-- `haddock-runner` installed (see [Installation](../installation.md))
+- `haddock-runner` installed (see [Installation](./installation.md))
 - HADDOCK3 properly installed and configured
 - Access to a computing environment with sufficient resources
 - Basic familiarity with command-line tools