Merge pull request #52 from Chaste/docker

Update PyChaste Docker Image

.github/workflows/pychaste-docker.yml

@@ -0,0 +1,40 @@
+name: pychaste-docker
+
+on:
+  workflow_dispatch:
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        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: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Build and load
+        uses: docker/build-push-action@v5
+        with:
+          context: ./infra/docker/
+          pull: true
+          load: true
+          tags: chaste/pychaste:latest
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: ./infra/docker/
+          pull: true
+          push: true
+          tags: chaste/pychaste:latest

infra/docker/Dockerfile

@@ -1,15 +1,20 @@
- FROM continuumio/miniconda
- RUN apt-get install build-essential lsb-release libgl1-mesa-dev:amd64 libxt-dev:amd64 libatlas-base-dev xvfb -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
- RUN conda config --add channels conda-forge && conda config --add channels jmsgrogan
- RUN conda install chaste && conda install libgcc --force && conda clean --yes --all && rm -rf /opt/conda/pkgs/*
- #RUN conda install vtk jupyter && conda install libgcc && conda clean --yes --all && rm -rf /opt/conda/pkgs/*
+FROM mambaorg/micromamba:1.5-jammy
 
- # Add Tini. Tini operates as a process subreaper for jupyter. This prevents
- # kernel crashes.
- ENV TINI_VERSION v0.6.0
- ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
- RUN chmod +x /usr/bin/tini 
+USER root
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        libgl1-mesa-dev \
+        libxt-dev \
+        xvfb && \
+    apt-get -y clean && \
+    rm -rf /var/cache/apt && \
+    rm -rf /var/lib/apt/lists/* && \
+    rm -rf /var/tmp/* && \
+    rm -rf /tmp/*
 
- ENTRYPOINT ["/usr/bin/tini", "--"]
+USER $MAMBA_USER
+RUN micromamba install -y -n base -c pychaste -c conda-forge -c bioconda chaste boost-cpp=1.74 notebook && \
+    micromamba clean --all --yes && \
+    rm -rf /opt/conda/pkgs/*
 
- CMD xvfb-run --server-args="-screen 0 1024x768x24" jupyter notebook --port=8888 --no-browser --ip=0.0.0.0
+CMD xvfb-run --server-args="-screen 0 1024x768x24" jupyter notebook --port=8888 --no-browser --ip=0.0.0.0

infra/docker/README.md

@@ -1,45 +1,31 @@
-# How to build the docker container
+# How to build the docker image
 
-The `pychaste` docker container is on the channel `jmsgrogan` on the Docker Hub. This directory contains the Dockerfile for setting up the container. Assuming Docker is set up, it can be built by doing:
+The `pychaste` docker image is on the channel `chaste` on the Docker Hub. This directory contains the Dockerfile for building the image. Assuming [Docker](https://www.docker.com) is set up, it can be built by running:
 
 ```bash
 [sudo] docker build -t pychaste .
 ```
 
-If you are happy with the package it can be tagged and uploaded. Do:
+If you are happy with the package it can be tagged and uploaded to Docker Hub.
+To find the image id, run:
 
 ```bash
 [sudo] docker images
 ```
 
-to find the image id. Then do:
+To tag the image with the `latest` tag and upload it to Docker Hub:
 
 ```bash
-[sudo] docker tag <image_id> jmsgrogan/pychaste:latest
+[sudo] docker tag <image_id> chaste/pychaste:latest
 docker login
-docker push jmsgrogan/pychaste
+docker push chaste/pychaste:latest
 ```
 
-## Preparing docker for the build
-
-To set up docker for the build do:
-
-```bash
-sudo apt-get update
-sudo apt-get install apt-transport-https ca-certificates
-sudo apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D
-echo "deb https://apt.dockerproject.org/repo ubuntu-xenial main" | sudo tee /etc/apt/sources.list.d/docker.list
-sudo apt-get update
-sudo apt-get install linux-image-extra-$(uname -r) linux-image-extra-virtuals
-sudo apt-get install docker-engine
-sudo service docker start
-```
-
-## Working with the package
+## Working with the local image
 
 ```bash
-[sudo] docker run -it -p 8888:8888 pychaste
+[sudo] docker run --init -it -p 8888:8888 pychaste
 ```
 
-Then go to [htpp://localhost::8888](htpp://localhost::8888) in a web browser.
+Then go to [http://localhost::8888](http://localhost::8888) in a web browser.