WIP: Fix dockerfile (#26)

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/main.yml

@@ -1,61 +1,63 @@
 name: Tests
-
-# Controls when the action will run.
-on:
-  # Triggers the workflow on push or pull request events but only for the main branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
   push:
     branches: [ main ]
   pull_request:
     branches: [ main ]
-
-  # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
+    inputs:
+      tags:
+        description: 'MNE-Python version (e.g. v0.23.0 or main)'
+        required: false
+        default: 'main'
 
 jobs:
   docker:
     runs-on: ubuntu-latest
     steps:
-
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
-
-      - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+      - uses: actions/checkout@v4
+      - uses: docker/login-action@v3
         with:
           registry: ghcr.io
-          username: ${{ github.repository_owner }}
+          username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
-
-      # Base
-
-      - name: Build base image
-        run: docker-compose build base
-
+      - name: Set env vars
+        run: |
+          set -eo pipefail
+          if [[ "${{ github.event.inputs.tags }}" != "" ]]; then
+            echo "MNE_VERSION=${{ github.event.inputs.tags }}" >> $GITHUB_ENV
+            echo "DOCKER_TAG=${{ github.event.inputs.tags }}" >> $GITHUB_ENV
+          else
+            echo "MNE_VERSION=main" >> $GITHUB_ENV
+            echo "DOCKER_TAG=latest" >> $GITHUB_ENV
+          fi
+          echo "Got MNE_VERSION=${MNE_VERSION}"
+          echo "Got DOCKER_TAG=${DOCKER_TAG}"
+      - run: docker compose build base --build-arg mne_v="$MNE_VERSION"
+      - run: docker tag mnetools/mne-python ghcr.io/mne-tools/mne-python:${DOCKER_TAG}
       - name: System info - base image
-        run: docker run mnetools/mne-python python -c "import mne; mne.sys_info()"
-
+        run: docker run mnetools/mne-python:${DOCKER_TAG} python -c "import mne; mne.sys_info()"
       - name: Run base test
-        run: docker run -v `pwd`:/opt/app/examples mnetools/mne-python python /opt/app/examples/tests/base.py
-
-      # Jupyter
-
-      - name: Build jupyter image
-        run: docker-compose build jupyter
-
+        run: docker run -v `pwd`:/opt/app/examples mnetools/mne-python:${DOCKER_TAG} python /opt/app/examples/tests/base.py
+      - run: docker compose build jupyter
+      - run: docker tag mnetools/mne-python-jupyter ghcr.io/mne-tools/mne-python-jupyter:${DOCKER_TAG}
       - name: System info - jupyter image
-        run: docker run mnetools/mne-python-jupyter ipython -c "import mne; mne.sys_info()"
-
+        run: docker run mnetools/mne-python-jupyter:${DOCKER_TAG} ipython -c "import mne; mne.sys_info()"
       - name: Run jupyter test
-        run: docker run -v `pwd`:/opt/app/examples mnetools/mne-python-jupyter ipython /opt/app/examples/tests/base.py
-
-      # Plot
-
-      - name: Build plot image
-        run: docker-compose build plot
-
+        run: docker run -v `pwd`:/opt/app/examples mnetools/mne-python-jupyter:${DOCKER_TAG} ipython /opt/app/examples/tests/base.py
+      - run: docker compose build plot
+      - run: docker tag mnetools/mne-python-plot ghcr.io/mne-tools/mne-python-plot:${DOCKER_TAG}
       - name: System info - plot image
-        run: docker run mnetools/mne-python-plot python -c "import mne; mne.sys_info()"
-
+        run: docker run mnetools/mne-python-plot:${DOCKER_TAG} python -c "import mne; mne.sys_info()"
       - name: Run plotting test
-        run: docker run -v `pwd`:/opt/app/examples mnetools/mne-python-plot python /opt/app/examples/tests/plot.py
+        run: docker run -v `pwd`:/opt/app/examples mnetools/mne-python-plot:${DOCKER_TAG} python /opt/app/examples/tests/plot.py
+      - name: Push images to github
+        run: |
+          set -exo pipefail
+          docker push ghcr.io/mne-tools/mne-python:${DOCKER_TAG}
+          docker push ghcr.io/mne-tools/mne-python-jupyter:${DOCKER_TAG}
+          docker push ghcr.io/mne-tools/mne-python-plot:${DOCKER_TAG}
+        if: github.repository == 'mne-tools/mne-docker' && (github.event_name == 'push' || github.event_name == 'workflow_dispatch')

base/Dockerfile

@@ -1,6 +1,7 @@
-FROM ubuntu:20.04
+# TODO: Use micromamba instead of bare image at some point
+FROM ubuntu:24.04
 
-ARG mne_v=v0.23.0
+ARG mne_v=v1.8.0
 
 ENV DEBIAN_FRONTEND=noninteractive
 
@@ -36,29 +37,41 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &
     rm -f ./Miniconda3-latest-Linux-x86_64.sh && \
     conda init
 SHELL ["/bin/bash", "--login", "-c"]
-
+RUN conda config --add channels conda-forge && \
+    conda config --remove channels defaults && \
+    conda config --set channel_priority strict && \
+    conda config --get channels
 RUN conda install --yes \
-    -c conda-forge \
-    python==3.9 \
+    python==3.12 \
     python-blosc \
     cytoolz \
-    dask==2021.4.0 \
+    dask \
     lz4 \
     nomkl \
-    numpy==1.21.0 \
-    pandas==1.3.0 \
-    tini==0.18.0 \
+    numpy \
+    pandas \
+    tini \
+    pooch \
+    bokeh \
+    joblib \
+    nibabel \
+    h5py \
+    s3fs \
+    matplotlib-base \
+    scikit-learn \
+    numba \
+    nilearn \
+    dipy \
+    h5io \
+    mamba \
+    conda-libmamba-solver \
     && conda clean -tipy \
     && find /opt/conda/ -type f,l -name '*.a' -delete \
     && find /opt/conda/ -type f,l -name '*.pyc' -delete \
     && find /opt/conda/ -type f,l -name '*.js.map' -delete \
     && find /opt/conda/lib/python*/site-packages/bokeh/server/static -type f,l -name '*.js' -not -name '*.min.js' -delete \
     && rm -rf /opt/conda/pkgs
 
-RUN pip install s3fs
-RUN pip install bokeh
-RUN pip install nibabel joblib h5py
-RUN pip install pooch
 RUN pip install https://github.com/mne-tools/mne-python/archive/${mne_v}.zip
 
 ENTRYPOINT ["tini", "-g", "--", "/usr/bin/prepare.sh"]

base/Dockerfile.jupyter

@@ -1,6 +1,6 @@
 FROM mnetools/mne-python
 
-RUN pip install jupyterlab ipywidgets ipyvtklink
+RUN conda install --yes jupyterlab ipywidgets ipympl
 
 EXPOSE 8888
 

base/Dockerfile.plot

@@ -5,21 +5,21 @@ ENV DEBIAN_FRONTEND=noninteractive
 # install xvfb
 USER root
 RUN apt-get update && \
-    apt-get install -y xvfb qt5-default && \
+    apt-get install -y xvfb && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
 USER $MNE_USER
 WORKDIR $HOME_DIR
 
-RUN pip install vtk pyvista pyvistaqt PyQt5 matplotlib
+RUN conda install --yes vtk pyvista pyvistaqt trame PySide6 qtpy mne-qt-browser trame-vtk trame-vuetify
 
 # setup environment for mne
 # MNE_3D_OPTION_ANTIALIAS is needed to avoid blank screenshots.
 # PYVISTA_OFF_SCREEN=true is *NOT* needed
 ENV \
-    MNE_3D_BACKEND=pyvista \
-    MNE_3D_OPTION_ANTIALIAS=false\
+    MNE_3D_BACKEND=pyvistaqt \
+    MNE_3D_OPTION_ANTIALIAS=false \
     START_XVFB=true
 
 ENTRYPOINT ["tini", "-g", "--", "/usr/bin/prepare.sh"]

base/prepare.sh

@@ -18,7 +18,7 @@ fi
 
 if [ "$EXTRA_CONDA_PACKAGES" ]; then
     echo "EXTRA_CONDA_PACKAGES environment variable found.  Installing."
-    /opt/conda/bin/conda install -y $EXTRA_CONDA_PACKAGES
+    /opt/conda/bin/conda install --yes $EXTRA_CONDA_PACKAGES
 fi
 
 if [ "$EXTRA_PIP_PACKAGES" ]; then