Add docker file and update README

.github/workflows/docker-image.yml

@@ -0,0 +1,74 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Create and publish a Docker image
+
+on:
+  push:
+    branches:
+      - "!*"
+    tags:
+      - "v*"
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+  LAB_NAME: lab
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for base-image
+        id: meta-base
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: ${{ github.event_name == 'push' }}
+          platforms: linux/amd64,linux/arm64
+          tags: ${{ steps.meta-base.outputs.tags }}
+          labels: ${{ steps.meta-base.outputs.labels }}
+          target: base
+
+      - name: Extract metadata (tags, labels) for lab images
+        id: meta-lab
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}-${{ env.LAB_NAME }}
+
+      - name: Build and push Docker lab image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: ${{ github.event_name == 'push' }}
+          platforms: linux/amd64,linux/arm64
+          tags: ${{ steps.meta-lab.outputs.tags }}
+          labels: ${{ steps.meta-lab.outputs.labels }}
+          target: lab

README.md

@@ -7,9 +7,11 @@ This repository contains supplementary code for reproducing results in the paper
 The code is heavily based on the library [`mps-motion`](https://github.com/ComputationalPhysiology/mps_motion). Please check out the [documentation](https://computationalphysiology.github.io/mps_motion/) in that library for more details.
 
 ## Running with binder
-If you want to run the examples without installing anything you can launch an interactive environment with Binder, by clicking the following button: TODO: Add button
+If you want to run the examples without installing anything you can launch an interactive environment with Binder, by clicking the following button [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComputationalPhysiology/automatic-motion-estimation-hiPSC-CM/HEAD)
 
 ## Running locally
+
+### Python virtual environment
 To run the notebooks locally, you first need to install the necessary requirements. There are two options. Either, you can create a virtual environment with python
 ```
 python3 -m venv venv
@@ -26,3 +28,17 @@ Next you install the dependencies
 ```
 python3 -m pip install -r requirements.txt
 ```
+
+### Docker
+
+We also provide two different docker images for you. In order to start a container you can use the docker run command. For example the command
+```
+docker run --rm -v $(pwd):/home/shared -w /home/shared -ti ghcr.io/computationalphysiology/automatic-motion-estimation-hiPSC-CM:latest
+```
+will run the latest version and share your current working directory with the container. The source code of the repository is located at `/repo` in the docker container.
+
+To run the notebooks, one can use `ghcr.io/computationalphysiology/automatic-motion-estimation-hiPSC-CM-lab:latest`, i.e
+```
+docker run -ti -p 8888:8888 --rm ghcr.io/computationalphysiology/automatic-motion-estimation-hiPSC-CM-lab:latest
+```
+to run interactively with Jupyter lab in browser.

docker/Dockerfile

@@ -0,0 +1,27 @@
+from ubuntu:22.04 as base
+
+RUN apt-get update && apt-get install -y python3-pip gcc python3-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+WORKDIR /repo
+
+COPY requirements.txt /repo
+
+RUN python3 -m pip install --upgrade pip
+RUN python3 -m pip install --no-cache-dir -r requirements.txt
+# Install the headless version of opencv in docker
+RUN python3 -m pip uninstall -y opencv-python opencv-contrib-python
+RUN python3 -m pip install --no-cache-dir opencv-python-headless opencv-contrib-python-headless
+
+
+COPY . /repo
+
+FROM base as lab
+
+# Had some issues with psutil (needed by jupyter) on aarch64, so need to install it from source
+RUN python3 -m pip install --no-cache-dir  psutil --no-binary=psutil
+RUN python3 -m pip install --no-cache-dir jupyter
+
+EXPOSE 8888/tcp
+ENTRYPOINT [ "jupyter", "lab", "--ip", "0.0.0.0", "--port", "8888", "--no-browser", "--allow-root"]

runtime.txt

@@ -0,0 +1 @@
+python-3.10