Merge branch 'main' into gradient_checks_only_for_lin_op

PTB-MR · Jan 13, 2025 · c3baccd · c3baccd
2 parents 4eccec5 + e029d5e
commit c3baccd
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diff --git a/.dockerignore b/.dockerignore
@@ -1,6 +1,5 @@
-.github
-.vscode
-binder
-examples
-docs
-tests
+.github
+.vscode
+examples
+docs
+tests
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -15,8 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     outputs:
       docker_toml: ${{ steps.filter.outputs.docker_toml }}
-      dockerfiles: ${{ steps.set-matrix.outputs.dockerfiles }}
-      imagenames: ${{ steps.set-matrix.outputs.imagenames }}
+      docker_tasks: ${{ steps.set-matrix.outputs.docker_tasks }}
     steps:
       - name: Checkout mrpro repo
         uses: actions/checkout@v4
@@ -39,20 +38,17 @@ jobs:
         id: set-matrix
         if: steps.filter.outputs.docker_toml == 'true' || github.event_name == 'push'
         run: |
-          cd ./docker/
-          ls
-          dockerfiles=$(ls Dockerfile_* | jq -R -s -c 'split("\n")[:-1]')
-          echo "dockerfiles: $dockerfiles"
-          echo "dockerfiles=$dockerfiles" >> $GITHUB_OUTPUT
-          imagenames=$(ls Dockerfile_* | sed -e 's/Dockerfile_/ghcr.io\/ptb-mr\/mrpro_/' | jq -R -s -c 'split("\n")[:-1]')
-          echo "image names: $imagenames"
-          echo "imagenames=$imagenames" >> $GITHUB_OUTPUT
+          # docker_tasks is a list of pairs (dictionaries) with keys 'filepath' and 'image_name' like:
+          # [{"filepath": "docker/Dockerfile_x1", "image_name": "ghcr.io/ptb-mr/mrpro_x1"}, ...]
+          docker_tasks=$(find docker -type f -name 'Dockerfile*' | jq -R -s -c 'split("\n")[:-1]' | \
+          jq -r -c 'map({filepath: ., image_name:  . | sub("docker/Dockerfile"; "ghcr.io\/ptb-mr\/mrpro")})')
+          echo "docker_tasks: $docker_tasks"
+          echo "docker_tasks=$docker_tasks" >> $GITHUB_OUTPUT
 
       - name: Dockerfile overview
         if: steps.filter.outputs.docker_toml == 'true' || github.event_name == 'push'
         run: |
-          echo "final list of dockerfiles: ${{ steps.set-matrix.outputs.dockerfiles }}"
-          echo "final list of images: ${{ steps.set-matrix.outputs.imagenames }}"
+          echo "final list of docker_tasks: ${{ steps.set-matrix.outputs.docker_tasks }}"
 
   push_test:
     name: Create test images and push to GCR
@@ -64,16 +60,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        dockerfile: ${{ fromJson(needs.get_dockerfiles.outputs.dockerfiles) }}
+        docker_task: ${{ fromJson(needs.get_dockerfiles.outputs.docker_tasks) }}
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Create image name
+      - name: Get image basename
         id: image_name
         run: |
-          dockerfile=${{ matrix.dockerfile }}
-          echo "image_name=${dockerfile/Dockerfile_/ghcr.io/ptb-mr/mrpro_}" >> $GITHUB_OUTPUT
+          echo "dockerfile_basename=$(basename ${{ matrix.docker_task.filepath }})" >> $GITHUB_OUTPUT
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
@@ -89,11 +84,11 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: .
-          cache-from: type=gha,scope=${{ matrix.dockerfile }}
-          cache-to: type=gha,mode=max,scope=${{ matrix.dockerfile }}
-          file: ./docker/${{ matrix.dockerfile }}
+          cache-from: type=gha,scope=$${{ steps.image_name.outputs.dockerfile_basename }})
+          cache-to: type=gha,mode=max,scope=${{ steps.image_name.outputs.dockerfile_basename }}
+          file: ${{ matrix.docker_task.filepath }}
           push: true
-          tags: ${{ steps.image_name.outputs.image_name }}:test
+          tags: ${{ matrix.docker_task.image_name }}:test
 
   test:
     name: Test docker containers
@@ -105,10 +100,10 @@ jobs:
       contents: write
     strategy:
       matrix:
-        imagename: ${{ fromJson(needs.get_dockerfiles.outputs.imagenames) }}
+        docker_task: ${{ fromJson(needs.get_dockerfiles.outputs.docker_tasks) }}
     # runs within Docker container
     container:
-      image: ${{ matrix.imagename }}:test
+      image: ${{ matrix.docker_task.image_name }}:test
       options: --user runner
 
     steps:
@@ -134,17 +129,11 @@ jobs:
       packages: write
     strategy:
       matrix:
-        dockerfile: ${{ fromJson(needs.get_dockerfiles.outputs.dockerfiles) }}
+        docker_task: ${{ fromJson(needs.get_dockerfiles.outputs.docker_tasks) }}
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Create image name
-        id: image_name
-        run: |
-          dockerfile=${{ matrix.dockerfile }}
-          echo "image_name=${dockerfile/Dockerfile_/ghcr.io/ptb-mr/mrpro_}" >> $GITHUB_OUTPUT
-
       - name: Login to GitHub Packages
         uses: docker/login-action@v3
         with:
@@ -154,6 +143,6 @@ jobs:
 
       - name: Pull and push Docker image with new tag
         run: |
-            docker pull ${{ steps.image_name.outputs.image_name }}:test
-            docker tag ${{ steps.image_name.outputs.image_name }}:test ${{ steps.image_name.outputs.image_name }}:latest
-            docker push ${{ steps.image_name.outputs.image_name }}:latest
+            docker pull ${{ matrix.docker_task.image_name }}:test
+            docker tag ${{ matrix.docker_task.image_name }}:test ${{ matrix.docker_task.image_name }}:latest
+            docker push ${{ matrix.docker_task.image_name}}:latest
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -71,9 +71,7 @@ jobs:
 
       - id: set-matrix
         run: |
-          cd ./examples/
-          ls
-          echo "notebooks=$(ls *.ipynb | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT
+          echo "notebooks=$(find examples -type f -name '*.ipynb' | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT
 
       - name: Notebook overview
         run: |
@@ -108,19 +106,37 @@ jobs:
         run: |
           echo "current jupyter-notebook: ${{ matrix.notebook }}"
 
+      - name: Add nb-myst download badge
+        run: |
+          notebook=${{ matrix.notebook }}
+          notebook_name=$(basename $notebook)
+          download_badge_md="[![Download notebook](https://img.shields.io/badge/Download-notebook-blue?logo=jupyter)](path:$notebook_name)"
+          python_command="import nbformat as nbf\n\
+          nb = nbf.read(open('$notebook'), as_version=4)\n\
+          # if the 1st cell is md and has colab text => add space after\n\
+          if nb['cells'][0]['cell_type'] == 'markdown' and 'colab' in nb['cells'][0]['source'].lower():\n\
+              nb['cells'][0]['source'] += ' '\n\
+          # if there is no md cell with colab => create empty md cell on top\n\
+          else:\n\
+              nb['cells'].insert(0, nbf.v4.new_markdown_cell())\n\
+          nb['cells'][0]['source'] += '$download_badge_md'\n\
+          nbf.write(nb, open('$notebook', 'w'))"
+
+          python -c "exec (\"$python_command\")"
+
       - name: Run notebook
         uses: fzimmermann89/run-notebook@v3
         env:
           RUNNER: ${{ toJson(runner) }}
         with:
-          notebook: ./examples/${{ matrix.notebook }}
+          notebook: ./${{ matrix.notebook }}
 
       - name: Get artifact names
         id: artifact_names
         run: |
           notebook=${{ matrix.notebook }}
-          echo "ARTIFACT_NAME=${notebook/.ipynb/}" >> $GITHUB_OUTPUT
-          echo "IPYNB_EXECUTED=${notebook}" >> $GITHUB_OUTPUT
+          echo "ARTIFACT_NAME=$(basename ${notebook/.ipynb})" >> $GITHUB_OUTPUT
+          echo "IPYNB_EXECUTED=$(basename $notebook)" >> $GITHUB_OUTPUT
 
       - name: Upload notebook
         uses: actions/upload-artifact@v4
@@ -155,6 +171,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           path: ./docs/source/_notebooks/
+          merge-multiple: true
 
       - name: Build docs
         run: |

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -15,18 +15,24 @@ jobs:
     outputs:
       imagenames: ${{ steps.set-matrix.outputs.imagenames }}
     steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
       - name: Retrieve Docker Image Names
         id: set-matrix
-        env:
-          GH_TOKEN: ${{ secrets.GHCR_TOKEN }}
         run: |
-          imagenames=$(curl -s --request GET \
-          --url "https://api.github.com/orgs/PTB-MR/packages?package_type=container" \
-          --header "Authorization: Bearer $GH_TOKEN"  | jq -r '.[].name')
+          # search for Dockerfile* in the docker directory, replace "Dockerfile" prefix with "mrpro" and to imagenames
+          imagenames=$(find docker -type f -name 'Dockerfile*' -exec basename {} \; | sed 's/^Dockerfile/mrpro/')
           echo "image names: $imagenames"
 
+          # if imagenames is empty - fail the workflow
+          if [ -z "$imagenames" ]; then
+            echo "No Dockerfiles found in the docker directory. Exiting..."
+            exit 1
+          fi
+
           imagenames_latest=()
-          for image in $(echo $imagenames)
+          for image in $imagenames
           do
             echo "checking $image ..."
             if docker manifest inspect "ghcr.io/ptb-mr/"$image":latest" >/dev/null; then

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -14,14 +14,14 @@ repos:
       - id: mixed-line-ending
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.8.6
     hooks:
       - id: ruff # linter
         args: [--fix]
       - id: ruff-format # formatter
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.27.0
+    rev: v1.29.4
     hooks:
       - id: typos
 
@@ -33,7 +33,7 @@ repos:
         exclude: ^tests/
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.1
     hooks:
       - id: mypy
         pass_filenames: false

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,54 @@
+abstract:
+    <p>MRpro is a MR image reconstruction and processing framework specifically
+    developed to work well with PyTorch. The data classes utilize torch tensors for
+    storing data such as MR raw data or reconstructed image data. Where possible batch
+    parallelisation of PyTorch is utilized to speed up image reconstruction.</p>
+authors:
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Zimmermann
+      given-names: Felix Frederik
+      orcid: 0000-0002-0862-8973
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Schuenke
+      given-names: Patrick
+      orcid: 0000-0002-3179-4830
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Brahma
+      given-names: Sherine
+      orcid: 0000-0003-4340-6513
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Guastini
+      given-names: Mara
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Hammacher
+      given-names: Johannes
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Kofler
+      given-names: Andreas
+      orcid: 0000-0002-7416-4433
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Kranich Redshaw
+      given-names: Catarina
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Lunin
+      given-names: Leonid
+      orcid: 0000-0001-6469-5532
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Martin
+      given-names: Stefan
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Schote
+      given-names: David
+      orcid: 0000-0003-3468-0676
+    - affiliation: Physikalisch-Technische Bundesanstalt
+      family-names: Kolbitsch
+      given-names: Christoph
+      orcid: 0000-0002-4355-8368
+cff-version: 1.2.0
+date-released: "2024-12-17"
+doi: 10.5281/zenodo.14509598
+license: Apache-2.0
+repository-code: https://github.com/PTB-MR/mrpro/
+title: MRpro - PyTorch-based MR image reconstruction and processing package
+type: software
+url: https://doi.org/10.5281/zenodo.14509598
diff --git a/README.md b/README.md
@@ -1,15 +1,24 @@
-# MRpro
+<h1 align="center">
 
-![Python](https://img.shields.io/badge/python-3.11%20%7C%203.12-blue)
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/source/_static/logo_white.svg">
+  <source media="(prefers-color-scheme: light)" srcset="docs/source/_static/logo.svg">
+  <img src="docs/source/_static/logo.svg" alt="MRpro logo" width="50%">
+</picture>
+
+</h1><br>
+
+![Python](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 ![Coverage Bagde](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/ckolbPTB/48e334a10caf60e6708d7c712e56d241/raw/coverage.json)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14509598.svg)](https://doi.org/10.5281/zenodo.14509598)
 
 MR image reconstruction and processing package specifically developed for PyTorch.
 
 - **Source code:** <https://github.com/PTB-MR/mrpro>
 - **Documentation:** <https://ptb-mr.github.io/mrpro/>
 - **Bug reports:** <https://github.com/PTB-MR/mrpro/issues>
-- **Try it out:** [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/PTB-MR/mrpro.git/main?labpath=examples)
+- **Try it out:** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrpro)
 
 ## Awards
 
@@ -84,5 +93,3 @@ We are looking forward to your contributions via Pull-Requests.
 4. Setup pre-commit hook: ``` pre-commit install ```
 
 Please look at our [contributor guide](https://ptb-mr.github.io/mrpro/contributor_guide.html) for more information on the repository structure, naming conventions, and other useful information.
-
-
diff --git a/binder/environment.yml b/binder/environment.yml