Merge branch 'update-MAGs-workflow' of https://github.com/paulzierep/iwc into update-MAGs-workflow

Author: paulzierep

.github/workflows/ci.yaml

@@ -7,7 +7,7 @@ on:
     types: [run-all-workflow-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_25.0
+  GALAXY_BRANCH: release_25.1
   MAX_CHUNKS: 40
 jobs:
   setup:

.github/workflows/gh-build-and-test.yml

@@ -35,8 +35,8 @@ jobs:
         run: npm install
         working-directory: ./website
 
-      - name: Build Nuxt 3 Static Site
-        run: npm run generate
+      - name: Build Astro Static Site
+        run: npm run build
         working-directory: ./website
 
       - name: Install Playwright

.github/workflows/gh-page-build.yml

@@ -34,12 +34,12 @@ jobs:
         run: npm install
         working-directory: ./website
 
-      - name: Build Nuxt 3 Static Site
-        run: npm run generate
+      - name: Build Astro Static Site
+        run: npm run build
         working-directory: ./website
 
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./website/.output/public
+          publish_dir: ./website/dist

.github/workflows/workflow_test.yml

@@ -22,7 +22,7 @@ jobs:
       python-version-list: "[\"3.11\"]"
       max-chunks: 4
       galaxy-fork: galaxyproject
-      galaxy-branch: release_25.0
+      galaxy-branch: release_25.1
 
   # Planemo lint the changed repositories
   lint:
@@ -69,7 +69,7 @@ jobs:
       python-version-list: "[\"3.11\"]"
       repository-list: ${{ needs.setup.outputs.repository-list }}
       galaxy-fork: galaxyproject
-      galaxy-branch: release_25.0
+      galaxy-branch: release_25.1
       check-outputs: false
 
   combine_outputs:

scripts/workflow_manifest.py

@@ -4,7 +4,7 @@
 import requests
 import re
 import shutil
-from urllib.parse import quote_plus
+from urllib.parse import quote_plus, quote
 from create_mermaid import walk_directory
 from planemo.galaxy.workflows import job_template
 
@@ -230,7 +230,10 @@ def path_to_location(input_item, root):
                 else:
                     # Create location URL from path for downloading files
                     relative_path = os.path.join(root.replace("./", ""), input_item["path"].lstrip("/"))
-                    input_item["location"] = f"https://raw.githubusercontent.com/galaxyproject/iwc/main/{relative_path}"
+                    # URL-encode the path to handle spaces and special characters
+                    # Use safe='/' to keep forward slashes unencoded as path separators
+                    encoded_path = quote(relative_path, safe='/')
+                    input_item["location"] = f"https://raw.githubusercontent.com/galaxyproject/iwc/main/{encoded_path}"
                     del input_item["path"]
             if "filetype" not in input_item:
                 # Add filetype if not present

website/.gitignore

@@ -1,24 +1,27 @@
-# Nuxt dev/build outputs
-.output
-.data
-.nuxt
-.nitro
-.cache
-dist
+# build output
+dist/
+.output/
 
-# Node dependencies
-node_modules
+# generated types
+.astro/
 
-# Logs
-logs
-*.log
+# dependencies
+node_modules/
 
-# Misc
-.DS_Store
-.fleet
-.idea
+# logs
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
 
-# Local env files
+# environment variables
 .env
-.env.*
-!.env.example
+.env.production
+
+# macOS-specific files
+.DS_Store
+
+# playwright
+test-results/
+test-output.txt
+playwright-report/

website/.prettierrc

@@ -1,4 +1,5 @@
 {
+    "plugins": ["prettier-plugin-astro"],
     "tabWidth": 4,
     "printWidth": 120,
     "bracketSameLine": true

website/README.md

@@ -1,83 +1,141 @@
-# Nuxt 3 Minimal Starter
+# IWC Website (Astro)
 
-Look at the [Nuxt 3 documentation](https://nuxt.com/docs/getting-started/introduction) to learn more.
+This is the Astro-based website for the Intergalactic Workflow Commission (IWC), showcasing the Galaxy Workflow Library.
 
-## Setup
+## 🚀 Quick Start
 
-Make sure to install the dependencies:
+### Prerequisites
+
+- Node.js 18+
+- npm or yarn
+
+### Installation
 
 ```bash
-# npm
 npm install
+```
 
-# pnpm
-pnpm install
-
-# yarn
-yarn install
+### Development
 
-# bun
-bun install
+```bash
+npm run dev
 ```
 
-## Build workflow manifest
+This starts the development server at `http://localhost:4321/`
 
-Build the workflow manifest file with
+### Building for Production
 
 ```bash
-python scripts/workflow_manifest.py
+npm run build
 ```
 
-## Development Server
+This generates a static site in the `dist/` directory.
 
-Start the development server on `http://localhost:3000`:
+### Preview Production Build
 
 ```bash
-# npm
-npm run dev
+npm run preview
+```
+
+### Testing
+
+```bash
+npm run test
+```
 
-# pnpm
-pnpm run dev
+Runs the Playwright E2E tests.
 
-# yarn
-yarn dev
+## 📁 Project Structure
 
-# bun
-bun run dev
+```
+├── public/               # Static assets
+│   ├── workflow_manifest.json  # Generated workflow metadata
+│   └── category-descriptions/  # Markdown descriptions for categories
+├── src/
+│   ├── components/       # Vue components (islands)
+│   │   ├── WorkflowCard.vue
+│   │   ├── Filters.vue
+│   │   ├── WorkflowGrid.vue
+│   │   ├── MarkdownRenderer.vue
+│   │   ├── GalaxyInstanceSelector.vue
+│   │   └── ...
+│   ├── layouts/          # Astro layouts
+│   │   └── BaseLayout.astro
+│   ├── models/           # TypeScript models
+│   │   └── workflow.ts
+│   ├── pages/            # Astro pages (file-based routing)
+│   │   ├── index.astro
+│   │   ├── about.astro
+│   │   ├── collection/[slug].astro
+│   │   └── workflow/[id].astro
+│   ├── stores/           # Nanostores for state management
+│   │   └── workflowStore.ts
+│   ├── utils/            # Utility functions
+│   │   ├── manifest.ts
+│   │   └── index.ts
+│   └── env.d.ts
+├── astro.config.mjs      # Astro configuration
+├── tailwind.config.ts    # Tailwind CSS configuration
+└── tsconfig.json         # TypeScript configuration
 ```
 
-## Production
+## 🧩 Key Technologies
 
-Build the application for production:
+- **Astro 5.2**: Static site generator with islands architecture
+- **Vue 3**: Interactive components using Vue islands
+- **Tailwind CSS**: Utility-first CSS framework
+- **Nanostores**: Lightweight state management
+- **TypeScript**: Type-safe development
+- **Fuse.js**: Fuzzy search
+- **Marked**: Markdown rendering
+- **Mermaid**: Diagram rendering
+- **Playwright**: E2E testing
 
-```bash
-# npm
-npm run build
+## 🏗️ Architecture
 
-# pnpm
-pnpm run build
+This site uses Astro's islands architecture, where:
 
-# yarn
-yarn build
+- Pages are pre-rendered at build time (SSG)
+- Interactive Vue components are hydrated on the client only where needed (`client:load`)
+- State management is handled by Nanostores (lighter than Pinia)
+- Workflow data is loaded from `workflow_manifest.json` generated by the Python scripts in the parent directory
 
-# bun
-bun run build
-```
+## 📝 Generating Workflow Manifest
 
-Locally preview production build:
+The workflow manifest must be generated before building the site:
 
 ```bash
-# npm
-npm run preview
+# From the repository root
+python scripts/workflow_manifest.py
+```
 
-# pnpm
-pnpm run preview
+This creates `website-astro/public/workflow_manifest.json` with metadata for all workflows.
 
-# yarn
-yarn preview
+## 🎨 Styling
 
-# bun
-bun run preview
-```
+The site uses a custom Galaxy color scheme defined in `tailwind.config.ts`:
+
+- **ebony-clay**: Dark navy (primary dark)
+- **bay-of-many**: Medium blue (primary)
+- **hokey-pokey**: Gold accent
+- **chicago**: Gray (secondary)
+
+## 🔄 Migration from Nuxt
+
+This site was migrated from Nuxt 3 to Astro for:
+
+- Better static site generation performance
+- Reduced JavaScript bundle size
+- Simpler architecture for a content-heavy site
+- Islands architecture for selective hydration
+
+Key changes:
+
+- Replaced Nuxt UI components with plain Tailwind
+- Replaced Pinia with Nanostores
+- Replaced Nuxt pages with Astro pages
+- Vue components remain mostly unchanged (used as islands)
+
+## 📄 License
 
-Check out the [deployment documentation](https://nuxt.com/docs/getting-started/deployment) for more information.
+See the parent repository for license information.