fixed orientation issues with DICOM to Nifti conversion #13
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| # This file was created automatically with `jupyter-book init --gh-pages` 🪄 💚 | |
| # Ensure your GitHub Pages settings for this repository are set to deploy with **GitHub Actions**. | |
| name: Jupyter Book HTML Deploy | |
| on: | |
| push: | |
| # Trigger on pushes to the actual default branch (master in this repo) | |
| branches: [ master ] | |
| workflow_dispatch: | |
| inputs: | |
| clean: | |
| description: "Clean _build before building" | |
| required: false | |
| type: boolean | |
| default: false | |
| env: | |
| # Custom domain already configured (neuraldatascience.io), serve from root | |
| BASE_URL: '' | |
| # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| # Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. | |
| # However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. | |
| concurrency: | |
| group: 'pages' | |
| cancel-in-progress: false | |
| jobs: | |
| build-deploy: | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup Node.js | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: '18' | |
| - name: Install MyST CLI | |
| run: npm install -g mystmd | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| # Install jupyter-book (latest 2.x) for myst-based site builds | |
| pip install jupyter-book | |
| - name: Show Jupyter Book version | |
| run: jupyter-book --version | |
| - name: (Optional) Clean previous builds | |
| if: inputs.clean == 'true' | |
| run: jupyter-book clean . | |
| - name: Build book (HTML site with MyST) | |
| run: myst build --html | |
| - name: List build output (debug) | |
| run: | | |
| ls -R _build/html | head -50 || echo "No html output found" | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: _build/html | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 |