Automatically build docker images for each Brian release

.github/workflows/publish_to_pypi.yml → .github/workflows/publish.yml

@@ -1,4 +1,4 @@
-name: Build and publish to TestPyPI or PyPI
+name: Build and publish
 on: [push, pull_request]
 
 jobs:
@@ -43,9 +43,9 @@ jobs:
           CIBW_TEST_COMMAND: python {project}/dev/continuous-integration/run_simple_test.py
           CIBW_TEST_REQUIRES: pytest
       - name: store distribution 📦
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: packages
+          name: packages-${{ matrix.os }}
           path: dist
 
   build-linux:
@@ -86,9 +86,9 @@ jobs:
           CIBW_TEST_COMMAND: python {project}/dev/continuous-integration/run_simple_test.py
           CIBW_TEST_REQUIRES: pytest
       - name: store distribution 📦
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: packages
+          name: packages-linux-${{ matrix.arch }}
           path: dist
 
   deploy_dev:
@@ -103,9 +103,10 @@ jobs:
       - build-linux
     steps:
       - name: load distribution 📦
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: packages
+          pattern: packages-*
+          merge-multiple: true
           path: dist/
       - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
@@ -124,9 +125,83 @@ jobs:
       - build-linux
     steps:
       - name: load distribution 📦
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: packages
+          pattern: packages-*
+          merge-multiple: true
           path: dist/
       - name: Publish distribution release 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
+
+  build-docker:
+    name: Build docker image
+    runs-on: ubuntu-latest
+    needs: build-linux
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      # https://github.com/actions/checkout/
+    - name: Docker meta
+      id: meta
+      uses: docker/metadata-action@v5
+      # https://github.com/docker/metadata-action
+      with:
+        images: |
+          briansimulator/brian
+        flavor: latest=true
+        tags: |
+          # type=semver,pattern={{raw}}
+          type=ref,event=tag
+        labels: |
+          org.opencontainers.image.title="Brian Docker Image"
+          org.opencontainers.image.description="Docker image for Brian - a free, open source simulator for spiking neural networks"
+          org.opencontainers.image.url=https://hub.docker.com/r/briansimulator/brian
+          org.opencontainers.image.source=https://github.com/brian-team/brian2
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v3
+      # https://github.com/docker/setup-qemu-action
+      with:
+        platforms: 'amd64,arm64'
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+      # https://github.com/docker/setup-buildx-action
+    - name: Login to DockerHub
+      uses: docker/login-action@v3
+      # https://github.com/docker/login-action
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+    - name: load Linux x86 distribution 📦
+      uses: actions/download-artifact@v4
+      with:
+        pattern: packages-linux-*
+        merge-multiple: true
+        path: packages
+    - run: |
+        mkdir dist
+        cp packages/Brian2*cp312-manylinux*_x86_64.whl dist
+        cp packages/Brian2*cp312-manylinux*_aarch64.whl dist
+    - name: Build (and potentially push) the Docker image
+      uses: docker/build-push-action@v5
+      # https://github.com/docker/build-push-action
+      with:
+        context: .
+        file: docker/Dockerfile
+        build-args: |
+            'BASE_IMAGE_TAG=3.12-bookworm'
+        platforms: 'amd64,arm64'
+        push: ${{ github.repository == 'brian-team/brian2' && startsWith(github.ref, 'refs/tags') }}
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}
+    - name: Push docker image to dev repository
+      if: ${{ github.repository == 'brian-team/brian2' && github.event_name == 'push' && !startsWith(github.ref, 'refs/tags') }} 
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        file: docker/Dockerfile
+        build-args: |
+            'BASE_IMAGE_TAG=3.12-bookworm'
+        platforms: 'amd64,arm64'
+        push: true
+        tags: briansimulator/brian-dev:dev-${{ github.ref_name }}
+        labels: ${{ steps.meta.outputs.labels }}        

README.rst

@@ -23,7 +23,6 @@ Stimberg, M, Brette, R, Goodman, DFM. “Brian 2, an Intuitive and Efficient Neu
 .. image:: https://img.shields.io/conda/vn/conda-forge/brian2.svg
         :target: https://anaconda.org/conda-forge/brian2
 
-
 .. image:: https://img.shields.io/debian/v/python3-brian/testing
    :alt: Debian package
    :target: https://packages.debian.org/testing/python3-brian
@@ -40,6 +39,13 @@ Stimberg, M, Brette, R, Goodman, DFM. “Brian 2, an Intuitive and Efficient Neu
    :alt: AUR version   
    :target: https://aur.archlinux.org/packages/python-brian2
 
+.. image:: https://github.com/brian-team/brian2/actions/workflows/publish.yml/badge.svg
+   :target: https://github.com/brian-team/brian2/actions/workflows/publish.yml
+   :alt: Publish status on GitHub Actions
+
+.. image:: https://img.shields.io/docker/pulls/briansimulator/brian
+   :alt: Docker Pulls
+
 
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8099373.svg
    :target: https://doi.org/10.5281/zenodo.8099373

docker/Dockerfile

@@ -0,0 +1,61 @@
+# docker buildx build --push --platform linux/amd64,linux/arm64/v8 -o type=image -t briansimulator/brian -f docker/Dockerfile .
+# docker run -it --init --rm -p 8888:8888 briansimulator/brian
+
+ARG BASE_IMAGE_TAG=3.12-slim-bookworm
+FROM python:${BASE_IMAGE_TAG}
+
+LABEL maintainer="Ben Evans <[email protected]>" \
+    org.opencontainers.image.vendor="The Brian Development Team" \
+    org.opencontainers.image.licenses="CeCILL 2.1" \
+    org.opencontainers.image.title="Brian Docker Image" \
+    org.opencontainers.image.description="Docker image for Brian - a free, open source simulator for spiking neural networks" \
+    org.opencontainers.image.homepage="https://briansimulator.org" \
+    org.opencontainers.image.url="https://hub.docker.com/r/briansimulator/brian" \
+    org.opencontainers.image.source="https://github.com/brian-team/brian2" \
+    org.opencontainers.image.documentation="https://brian2.readthedocs.io/"
+
+# Install dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    g++ \
+    git \
+    libgsl-dev \
+    sudo \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy wheels into the image
+COPY dist /tmp/dist
+
+# Install Brian2 and recommended packages
+RUN python -m pip install --no-cache-dir --only-binary=:all: \
+    scipy \
+    matplotlib \
+    jupyterlab \
+    pytest \
+    pytest-xdist \
+    && python -m pip install /tmp/dist/Brian2*_$(uname -m).whl brian2tools \
+    && rm -rf /tmp/dist
+
+# Create a non-root user
+ARG USER="monty" \
+    GROUP="monty" \
+    PASSWORD="monty"
+RUN groupadd ${GROUP} && \
+    useradd -ms /bin/bash -g ${GROUP} -G sudo ${USER} && \
+    echo "${USER}:${PASSWORD}" | chpasswd
+ENV HOME="/home/${USER}"
+RUN chown -R ${USER}:${USER} ${HOME}
+USER ${USER}
+
+# Copy tutorial notebooks and example scripts to home directory
+WORKDIR ${HOME}
+RUN git clone https://github.com/brian-team/brian2.git \
+    && mv brian2/examples examples \
+    && mv brian2/tutorials tutorials \
+    && chmod -R +x tutorials \
+    && chmod -R +x examples \
+    && find . -name '*.ipynb' -exec jupyter trust {} \; \
+    && rm -rf brian2
+
+EXPOSE 8888
+CMD ["jupyter", "lab", "--ip=0.0.0.0", "--no-browser"]

docker/README.md

@@ -0,0 +1,72 @@
+# Docker instructions
+
+## Run docker image
+To run the docker image, you can use
+
+`docker run -it --init -p 8888:8888 briansimulator/brian`
+
+This will start a JupyterLab instance inside the container, which you can access from your local browser via the last link
+printed to the terminal (`http://127.0.0.1:8888/lab?token=…`) 
+
+Or if you prefer a simple `bash` terminal rather than JupyterLab:
+
+`docker run -it --init briansimulator/brian /bin/bash`
+
+Or to run the tests:
+
+`docker run -it --init --rm briansimulator/brian python -c 'import brian2; brian2.test(test_standalone="cpp_standalone")'`
+
+## Build docker image
+To build the docker image locally, follow the following instructions:
+
+### Build package wheel
+You need to first build the package wheel(s) for linux using [`cibuildwheel`](https://cibuildwheel.readthedocs.io). Install it via
+`pip install cibuildwheel` (or use `pipx`)
+
+#### Build wheel for local architecture
+Run `cibuildwheel` to build a package for your architecture:
+```
+export CIBW_BUILD='cp312-manylinux*'
+cibuildwheel --platform linux --arch auto64 --output-dir dist
+```
+
+#### Build multi-arch wheel
+First install `qemu` for cross-compilation, e.g. on Debian/Ubuntu:
+
+`sudo apt install qemu-user-static`
+
+Then, run
+```
+export CIBW_BUILD='cp312-manylinux*'
+cibuildwheel --platform linux --arch auto64,aarch64 --output-dir dist
+```
+
+### Build docker image
+
+You can then build the docker image via
+
+`docker build -t briansimulator/brian -f docker/Dockerfile .`
+
+Alternatively, to test multi-architecture builds and push to docker hub, first login:
+
+`docker login`
+
+Create a new builder that uses the docker-container driver (only needed once):
+```
+docker buildx create \                                                                                                                
+  --name container \
+  --driver=docker-container \
+  default
+```
+Then execute:
+
+```
+docker buildx build \
+  --builder=container \
+  --push \
+  --platform linux/amd64,linux/arm64/v8 \
+  -o type=image \
+  -t briansimulator/brian \
+  -f docker/Dockerfile \
+  .
+```