Merge branch 'main' into MSEDataConsistency

PTB-MR · Nov 13, 2024 · 57c3193 · 57c3193
2 parents 7603375 + 798f1e2
commit 57c3193
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diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,6 @@
+.github
+.vscode
+binder
+examples
+docs
+tests
diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -1,4 +1,4 @@
-name: Publish to PyPI
+name: Build and Deploy Package
 
 on:
   push:
@@ -7,21 +7,31 @@ on:
 
 jobs:
   build-testpypi-package:
-    name: Modify version and build package for TestPyPI
+    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: Checkout code
-        uses: actions/checkout@v4
-
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.x"
 
-      - name: Set environment variable for version suffix
+      - 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=$(cat src/mrpro/VERSION)
@@ -30,12 +40,12 @@ jobs:
           echo "suffix=$SUFFIX" >> $GITHUB_OUTPUT
           echo "version=$VERSION" >> $GITHUB_OUTPUT
 
-      - name: Build package with version suffix
+      - name: Build Package
         run: |
           python -m pip install --upgrade build
           python -m build
 
-      - name: Store TestPyPi distribution
+      - name: Upload TestPyPI Distribution Artifact
         uses: actions/upload-artifact@v4
         with:
           name: testpypi-package-distribution
@@ -46,6 +56,7 @@ jobs:
     needs:
       - build-testpypi-package
     runs-on: ubuntu-latest
+    if: needs.build-testpypi-package.outputs.version_changed == 'true'
 
     environment:
       name: testpypi
@@ -55,7 +66,7 @@ jobs:
       id-token: write
 
     steps:
-      - name: Download TestPyPi distribution
+      - name: Download TestPyPI Distribution
         uses: actions/download-artifact@v4
         with:
           name: testpypi-package-distribution
@@ -68,7 +79,7 @@ jobs:
           verbose: true
 
   test-install-from-testpypi:
-    name: Test installation from TestPyPI
+    name: Test Installation from TestPyPI
     needs:
       - testpypi-deployment
       - build-testpypi-package
@@ -83,40 +94,48 @@ jobs:
         run: |
           VERSION=${{ needs.build-testpypi-package.outputs.version }}
           SUFFIX=${{ needs.build-testpypi-package.outputs.suffix }}
-          python -m pip install mrpro==$VERSION$SUFFIX --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/
+          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
+    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
+      - name: Checkout Code
         uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.x"
 
-      - name: Install setuptools_git_versioning
+      - name: Install Automatic Versioning Tool
         run: |
           python -m pip install setuptools-git-versioning
 
-      - name: Get current version
+      - name: Get Current Version
         id: get_version
         run: |
           VERSION=$(python -m setuptools_git_versioning)
           echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
 
-      - name: Build package
+      - name: Build Package
         run: |
           python -m pip install --upgrade build
           python -m build
 
-      - name: Store PyPi distribution
+      - name: Store PyPI Distribution
         uses: actions/upload-artifact@v4
         with:
           name: pypi-package-distribution
@@ -138,13 +157,13 @@ jobs:
       id-token: write
 
     steps:
-      - name: Download PyPi distribution
+      - name: Download PyPI Distribution
         uses: actions/download-artifact@v4
         with:
           name: pypi-package-distribution
           path: dist/
 
-      - name: Create tag
+      - name: Create Tag
         uses: actions/github-script@v7
         with:
           script: |
@@ -155,7 +174,7 @@ jobs:
               sha: context.sha
             })
 
-      - name: Create release
+      - name: Create Release
         uses: actions/github-script@v7
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"

diff --git a/.github/workflows/docker.yml b/.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

diff --git a/.github/workflows/docs.yml b/.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:

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -2,17 +2,21 @@ name: PyTest
 
 on:
   pull_request:
+  push:
+    branches:
+      - main
 
 jobs:
   get_dockerfiles:
-    name: Get list of dockerfiles for different containers
+    name: Get List of Dockerfiles for Containers
     runs-on: ubuntu-latest
     permissions:
       packages: read
     outputs:
       imagenames: ${{ steps.set-matrix.outputs.imagenames }}
     steps:
-      - id: set-matrix
+      - name: Retrieve Docker Image Names
+        id: set-matrix
         env:
           GH_TOKEN: ${{ secrets.GHCR_TOKEN }}
         run: |
@@ -35,57 +39,56 @@ jobs:
           echo "image names with tag latest: $imagenames_latest"
           echo "imagenames=$imagenames_latest" >> $GITHUB_OUTPUT
 
-      - name: Dockerfile overview
+      - name: Dockerfile Overview
         run: |
-          echo "final list of images with tag latest: ${{ steps.set-matrix.outputs.imagenames }}"
+          echo "Final list of images with tag latest: ${{ steps.set-matrix.outputs.imagenames }}"
 
   test:
-    name: Run tests and get coverage report
+    name: Run Tests and Coverage Report
     needs: get_dockerfiles
     runs-on: ubuntu-latest
     permissions:
       pull-requests: write
       contents: write
     strategy:
+      fail-fast: false
       matrix:
         imagename: ${{ fromJson(needs.get_dockerfiles.outputs.imagenames) }}
-    # runs within Docker container
     container:
       image: ghcr.io/ptb-mr/${{ matrix.imagename }}:latest
       options: --user runner
-
     steps:
-      - name: Checkout repo
+      - name: Checkout Repository
         uses: actions/checkout@v4
 
-      - name: Install mrpro and dependencies
-        run: pip install --upgrade --upgrade-strategy "eager" .[test]
+      - name: Install MRpro and Dependencies
+        run: pip install --upgrade --upgrade-strategy eager .[test]
 
-      - name: Install pytest-github-actions-annotate-failures plugin
+      - name: Install PyTest GitHub Annotation Plugin
         run: pip install pytest-github-actions-annotate-failures
 
-      - name: Run PyTest
+      - name: Run PyTest and Generate Coverage Report
         run: |
-          pytest -n 4 -m "not cuda" --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=mrpro | tee pytest-coverage.txt
+          pytest -n 4 -m "not cuda" --junitxml=pytest.xml \
+          --cov-report=term-missing:skip-covered --cov=mrpro | tee pytest-coverage.txt
 
-      - name: Check for pytest.xml
+      - name: Verify PyTest XML Output
         run: |
-          if [ -f pytest.xml ]; then
-            echo "pytest.xml file found. Continuing..."
-          else
-            echo "pytest.xml file not found. Please check previous 'Run PyTest' section for errors."
+          if [ ! -f pytest.xml ]; then
+            echo "PyTest XML report not found. Please check the previous 'Run PyTest' step for errors."
             exit 1
           fi
 
-      - name: Pytest coverage comment
+      - name: Post PyTest Coverage Comment
         id: coverageComment
         uses: MishaKav/pytest-coverage-comment@v1.1.53
         with:
           pytest-coverage-path: ./pytest-coverage.txt
           junitxml-path: ./pytest.xml
 
-      - name: Create the Badge
+      - name: Create Coverage Badge on Main Branch Push
         uses: schneegans/dynamic-badges-action@v1.7.0
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
         with:
           auth: ${{ secrets.GIST_SECRET }}
           gistID: 48e334a10caf60e6708d7c712e56d241
@@ -95,12 +98,12 @@ jobs:
           color: ${{ steps.coverageComment.outputs.color }}
           namedLogo: python
 
-      - name: Set pipeline status
+      - name: Set Pipeline Status Based on Test Results
         if: steps.coverageComment.outputs.errors != 0 || steps.coverageComment.outputs.failures != 0
         uses: actions/github-script@v7
         with:
           script: |
-            core.setFailed('PyTest workflow failed with ${{ steps.coverageComment.outputs.errors }} errors and ${{ steps.coverageComment.outputs.failures }} failures.')
+            core.setFailed("PyTest workflow failed with ${{ steps.coverageComment.outputs.errors }} errors and ${{ steps.coverageComment.outputs.failures }} failures.")
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,10 +3,9 @@
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
-      - id: check-docstring-first
       - id: check-merge-conflict
       - id: check-yaml
       - id: check-toml
@@ -15,19 +14,26 @@ repos:
       - id: mixed-line-ending
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.2
     hooks:
       - id: ruff # linter
         args: [--fix]
       - id: ruff-format # formatter
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.25.0
+    rev: v1.27.0
     hooks:
       - id: typos
 
+  - repo: https://github.com/fzimmermann89/check_all
+    rev: v1.0
+    hooks:
+      - id: check-init-all
+        args: [--double-quotes]
+        exclude: ^tests/
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
       - id: mypy
         pass_filenames: false
@@ -37,19 +43,21 @@ repos:
           - numpy
           - torch>=2.4.0
           - types-requests
+          - typing-extensions
           - einops
           - pydicom
           - matplotlib
           - pytest
           - xsdata
           - "--index-url=https://download.pytorch.org/whl/cpu"
           - "--extra-index-url=https://pypi.python.org/simple"
+
 ci:
-    autofix_commit_msg: |
-        [pre-commit] auto fixes from pre-commit hooks
-    autofix_prs: false
-    autoupdate_branch: ''
-    autoupdate_commit_msg: '[pre-commit] pre-commit autoupdate'
-    autoupdate_schedule: monthly
-    skip: [mypy]
-    submodules: false
+  autofix_commit_msg: |
+    [pre-commit] auto fixes from pre-commit hooks
+  autofix_prs: false
+  autoupdate_branch: ""
+  autoupdate_commit_msg: "[pre-commit] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: [mypy]
+  submodules: false
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -4,7 +4,7 @@
         "davidanson.vscode-markdownlint",
         "editorconfig.editorconfig",
         "kevinrose.vsc-python-indent",
-        "ms-python.black-formatter",
+        "charliermarsh.ruff",
         "ms-python.isort",
         "ms-python.python",
         "ms-python.vscode-pylance",