Merge pull request #7 from bloyl/viz

add 2d/3d plotting support to base Dockerfile

.github/workflows/main.yml

@@ -1,6 +1,6 @@
 name: CI
 
-# Controls when the action will run. 
+# Controls when the action will run.
 on:
   # Triggers the workflow on push or pull request events but only for the main branch
   push:
@@ -10,12 +10,12 @@ on:
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-  
+
 jobs:
   docker:
     runs-on: ubuntu-latest
     steps:
-    
+
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0
@@ -28,5 +28,8 @@ jobs:
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Build docker image
+      - name: Build docker images
         run: docker-compose build
+
+      - name: System info
+        run: docker run mnetools/mne-python python -c "import mne; mne.sys_info()"

base/Dockerfile

@@ -1,4 +1,39 @@
-FROM continuumio/miniconda3:4.8.2
+FROM ubuntu:20.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+ARG MNE_USER="mne_user"
+ARG HOME_DIR="/home/${MNE_USER}"
+ENV MNE_USER=${MNE_USER}
+ENV HOME_DIR=${HOME_DIR}
+
+ARG CONDA_DIR="/opt/conda/"
+
+# install xvfb
+RUN apt-get update && \
+    apt-get install -y wget && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# setup entry point
+COPY prepare.sh /usr/bin/prepare.sh
+RUN chmod a+x /usr/bin/prepare.sh
+
+RUN chmod 777 /opt
+
+# setup mne user
+RUN useradd -ms /bin/bash -d ${HOME_DIR} ${MNE_USER}
+USER $MNE_USER
+WORKDIR $HOME_DIR
+
+# setup conda
+ENV PATH="${CONDA_DIR}/bin:${PATH}"
+ARG PATH="${CONDA_DIR}/bin:${PATH}"
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    sh ./Miniconda3-latest-Linux-x86_64.sh -b -p ${CONDA_DIR} && \
+    rm -f ./Miniconda3-latest-Linux-x86_64.sh && \
+    conda init
+SHELL ["/bin/bash", "--login", "-c"]
 
 RUN conda install --yes \
     -c conda-forge \
@@ -19,11 +54,7 @@ RUN conda install --yes \
     && rm -rf /opt/conda/pkgs
 
 RUN pip install s3fs
-RUN pip install mne
 RUN pip install bokeh
-
-COPY prepare.sh /usr/bin/prepare.sh
-
-RUN mkdir /opt/app
+RUN pip install nibabel joblib h5py mne
 
 ENTRYPOINT ["tini", "-g", "--", "/usr/bin/prepare.sh"]

base/Dockerfile.plot

@@ -0,0 +1,25 @@
+FROM mnetools/mne-python
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# install xvfb
+USER root
+RUN apt-get update && \
+    apt-get install -y xvfb qt5-default && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+USER $MNE_USER
+WORKDIR $HOME_DIR
+
+RUN pip install vtk pyvista pyvistaqt PyQt5 matplotlib nibabel joblib h5py mne
+
+# 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\
+    START_XVFB=true
+
+ENTRYPOINT ["tini", "-g", "--", "/usr/bin/prepare.sh"]

base/prepare.sh

@@ -26,5 +26,13 @@ if [ "$EXTRA_PIP_PACKAGES" ]; then
     /opt/conda/bin/pip install $EXTRA_PIP_PACKAGES
 fi
 
+if [ "$START_XVFB" ]; then
+    /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid \
+        --make-pidfile --background --exec /usr/bin/Xvfb -- :99 \
+        -screen 0 1400x900x24 -ac +extension GLX +render -noreset
+    sleep 3
+    export DISPLAY=:99
+fi
+
 # Run extra commands
 exec "$@"

docker-compose.yml

@@ -1,21 +1,35 @@
 version: "3.1"
 
 services:
-  scheduler:
+  base:
     build:
       context: ./base
       dockerfile: Dockerfile
     image: mnetools/mne-python
+
+  scheduler:
+    depends_on:
+      - base
+    image: mnetools/mne-python
     hostname: mne-dask-scheduler
     ports:
       - "8786:8786"
       - "8787:8787"
     command: ["dask-scheduler"]
 
   worker:
-    build:
-      context: ./base
-      dockerfile: Dockerfile
+    depends_on:
+      - base
     image: mnetools/mne-python
     hostname: mne-dask-worker
     command: ["dask-worker", "tcp://scheduler:8786"]
+
+  worker_viz:
+    depends_on:
+        - base
+    build:
+      context: ./base
+      dockerfile: Dockerfile.plot
+    image: mnetools/mne-python-plot
+    hostname: mne-dask-worker-plot
+    command: ["dask-worker", "tcp://scheduler:8786"]