gh actions build/push image

.github/workflows/image.yml

+name: Create and publish a Docker image
+
+on:
+  push:
+    branches: ['dev']
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

+FROM ubuntu:20.04
+LABEL maintainer="marmaduke.woodman@univ-amu.fr"
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+WORKDIR /usr/local
+
+RUN apt-get update \
+ && apt-get install -y libnss3-dev libx11-xcb1 libxcb-dri3-0 libxcomposite1 \
+	libxcursor1 libxdamage1 libxfixes3 libxi6 libxtst6 libatk1.0-0 libatk-bridge2.0-0 \
+	libgdk-pixbuf2.0-0 libgtk-3-0 libgtk-3-0 libpangocairo-1.0-0 libpango-1.0-0 libcairo2 \
+	libdrm2 libgbm1 libasound2 libatspi2.0-0 curl git build-essential tcsh perl nodejs \
+	python2 wget datalad bc libglu1-mesa-dev unzip
+
+RUN wget -q https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz \
+ && tar xzf freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz \
+ && rm freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz
+
+RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py \
+ && echo "" | python2 fslinstaller.py
+
+RUN curl -LO https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+ && bash Miniconda3-latest-Linux-x86_64.sh -b -p $PWD/conda \
+ && rm Miniconda3-latest-Linux-x86_64.sh \
+ && export PATH=$PWD/conda/bin:$PATH \
+ && conda install -y jupyter numba scipy matplotlib \
+ && conda install -y -c mrtrix3 mrtrix3 \
+ && pip install tvb-data tvb-library tqdm pybids siibra requests pyunicore mne nilearn pyvista ipywidgets cmdstanpy \
+ && install_cmdstan \
+ && mv /root/.cmdstan $PWD/cmdstan
+
+ENV PATH=/usr/local/conda/bin:$PATH
+ENV FREESURFER_HOME=/usr/local/freesurfer
+
+# TODO setup env automatically on entry