Merge branch 'main' into fista

.dockerignore

@@ -0,0 +1,6 @@
+.github
+.vscode
+binder
+examples
+docs
+tests

.github/workflows/deployment.yml

@@ -0,0 +1,202 @@
+name: Build and Deploy Package
+
+on:
+  push:
+    paths:
+      - src/mrpro/VERSION
+
+jobs:
+  build-testpypi-package:
+    name: Build Package for TestPyPI
+    runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.set_suffix.outputs.version }}
+      suffix: ${{ steps.set_suffix.outputs.suffix }}
+      version_changed: ${{ steps.changes.outputs.version_changed }}
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Check if VERSION file is modified compared to main
+        uses: dorny/paths-filter@v3
+        id: changes
+        with:
+          base: main
+          filters: |
+            version_changed:
+              - 'src/mrpro/VERSION'
+
+      - name: Set Version Suffix
+        id: set_suffix
+        run: |
+          VERSION=$(cat src/mrpro/VERSION)
+          SUFFIX=rc$(date +%s)
+          echo "MRPROVERSIONSUFFIX=$SUFFIX" >> $GITHUB_ENV
+          echo "suffix=$SUFFIX" >> $GITHUB_OUTPUT
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Build Package
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - name: Upload TestPyPI Distribution Artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: testpypi-package-distribution
+          path: dist/
+
+  testpypi-deployment:
+    name: Deploy to TestPyPI
+    needs:
+      - build-testpypi-package
+    runs-on: ubuntu-latest
+    if: needs.build-testpypi-package.outputs.version_changed == 'true'
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/mrpro
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download TestPyPI Distribution
+        uses: actions/download-artifact@v4
+        with:
+          name: testpypi-package-distribution
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+
+  test-install-from-testpypi:
+    name: Test Installation from TestPyPI
+    needs:
+      - testpypi-deployment
+      - build-testpypi-package
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install MRpro from TestPyPI
+        run: |
+          VERSION=${{ needs.build-testpypi-package.outputs.version }}
+          SUFFIX=${{ needs.build-testpypi-package.outputs.suffix }}
+          for i in {1..3}; do
+            if python -m pip install mrpro==$VERSION$SUFFIX --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/; then
+              echo "Package installed successfully."
+              break
+            else
+              echo "Attempt $i failed. Retrying in 10 seconds..."
+              sleep 10
+            fi
+          done
+
+  build-pypi-package:
+    name: Build Package for PyPI
+    runs-on: ubuntu-latest
+    needs:
+      - test-install-from-testpypi
+    outputs:
+      version: ${{ steps.get_version.outputs.version }}
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install Automatic Versioning Tool
+        run: |
+          python -m pip install setuptools-git-versioning
+
+      - name: Get Current Version
+        id: get_version
+        run: |
+          VERSION=$(python -m setuptools_git_versioning)
+          echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Build Package
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - name: Store PyPI Distribution
+        uses: actions/upload-artifact@v4
+        with:
+          name: pypi-package-distribution
+          path: dist/
+
+  pypi-deployment:
+    name: Deploy to PyPI
+    needs:
+      - build-pypi-package
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/project/mrpro
+
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+      - name: Download PyPI Distribution
+        uses: actions/download-artifact@v4
+        with:
+          name: pypi-package-distribution
+          path: dist/
+
+      - name: Create Tag
+        uses: actions/github-script@v7
+        with:
+          script: |
+            github.rest.git.createRef({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              ref: 'refs/tags/v${{ needs.build-pypi-package.outputs.version }}',
+              sha: context.sha
+            })
+
+      - name: Create Release
+        uses: actions/github-script@v7
+        with:
+          github-token: "${{ secrets.GITHUB_TOKEN }}"
+          script: |
+            github.rest.repos.createRelease({
+              draft: false,
+              generate_release_notes: true,
+              name: "v${{ needs.build-pypi-package.outputs.version }}",
+              owner: context.repo.owner,
+              prerelease: false,
+              repo: context.repo.repo,
+              tag_name: "v${{ needs.build-pypi-package.outputs.version }}",
+            });
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://upload.pypi.org/legacy/
+          verbose: true
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+
+  # Cancel in-progress runs when a new workflow with the same group name is triggered
+  cancel-in-progress: true

.github/workflows/docker.yml

@@ -62,6 +62,7 @@ jobs:
     permissions:
       packages: write
     strategy:
+      fail-fast: false
       matrix:
         dockerfile: ${{ fromJson(needs.get_dockerfiles.outputs.dockerfiles) }}
     steps:
@@ -87,7 +88,9 @@ jobs:
       - name: Build and push Docker image
         uses: docker/build-push-action@v6
         with:
-          context: ./docker
+          context: .
+          cache-from: type=gha,scope=${{ matrix.dockerfile }}
+          cache-to: type=gha,mode=max,scope=${{ matrix.dockerfile }}
           file: ./docker/${{ matrix.dockerfile }}
           push: true
           tags: ${{ steps.image_name.outputs.image_name }}:test

.github/workflows/docs.yml

@@ -92,6 +92,7 @@ jobs:
       image: ghcr.io/ptb-mr/mrpro_py311:latest
       options: --user root
     strategy:
+      fail-fast: false
       matrix:
         notebook: ${{ fromJson(needs.get_notebooks.outputs.notebooks) }}
     steps:
@@ -137,6 +138,9 @@ jobs:
     container:
       image: ghcr.io/ptb-mr/mrpro_py311:latest
       options: --user runner
+    permissions:
+      pull-requests: write
+      contents: write
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -181,21 +185,57 @@ jobs:
           done
 
       - name: Build docs
-        run: sphinx-build -b html ./docs/source ./docs/build/html
-
-      - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v4
-        with:
-          publish_branch: github-pages
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs/build/html
-        if: github.event_name != 'pull_request'
+        run: |
+          sphinx-build -b html ./docs/source ./docs/build/html
+          rm -rf ./docs/build/html/.doctrees
 
       - name: Save Documentation
+        id: save_docu
         uses: actions/upload-artifact@v4
         with:
           name: Documentation
           path: docs/build/html/
+
+      - run: echo 'Artifact url ${{ steps.save_docu.outputs.artifact-url }}'
+
+      - run: echo 'Event number ${{ github.event.number }}'
+
+      - run: echo 'Event name ${{github.event_name}}'
+
+      - name: Update PR with link to summary
+        if: github.event_name == 'pull_request'
+        uses: edumserrano/find-create-or-update-comment@v3
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          body-includes: '<!-- documentation build ${{ github.event.number }} -->'
+          comment-author: 'github-actions[bot]'
+          body: |
+            <!-- documentation build ${{ github.event.number }} -->
+            ### :books: Documentation
+            :file_folder: [Download as zip](${{ steps.save_docu.outputs.artifact-url }})
+            :mag: [View online](https://zimf.de/zipserve/${{ steps.save_docu.outputs.artifact-url }}/)
+          edit-mode: replace
+
+      - name: Upload pages
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html/
+        if: github.event_name != 'pull_request'
+
+  deploy:
+    if: github.ref == 'refs/heads/main'
+    permissions:
+        pages: write   
+        id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: create_documentation
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}