add docker workflow

- adds dockerfiles
- adds pip requirements, modifies existing requirements (add cmake)
- adds composite github action
- adds dockerignore file

.dockerignore

@@ -0,0 +1,6 @@
+/docs/
+/.github/
+/examples/
+/LICENSE
+/.readthedocs.yml
+/.gitignore

.github/actions/docker_setup/action.yml

@@ -0,0 +1,32 @@
+name: 'Setup Workflow'
+description: 'Set up environment and Docker settings'
+
+inputs:
+  github_event_name:
+    description: 'GitHub Event Name'
+    required: true
+  DOCKERHUB_USERNAME:
+    description: 'DockerHub Username'
+    required: true
+  DOCKERHUB_TOKEN:
+    description: 'DockerHub Token'
+    required: true
+  DOCKERHUB_ORG:
+    description: 'DockerHub Organization'
+    required: true
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Set DOCKERHUB_ORG
+      run: |
+        echo "DOCKERHUB_ORG=${{ inputs.DOCKERHUB_ORG == '' && 'openchemistry' || inputs.DOCKERHUB_ORG }}" >> $GITHUB_ENV
+      shell: bash
+    - name: Login to Docker Hub
+      uses: docker/login-action@v2
+      if: ${{ github.event_name != 'pull_request' }}
+      with:
+        username: ${{ inputs.DOCKERHUB_USERNAME }}
+        password: ${{ inputs.DOCKERHUB_TOKEN }}
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2

.github/workflows/docker.yml

@@ -0,0 +1,137 @@
+name: docker
+
+on:
+  push:
+    branches:
+      # - "master"
+      - 'gha-final'
+  pull_request:
+    branches:
+      - 'master'
+
+jobs:
+  # Builds base image for stempy of various verions if Dockerfile.base has changed
+  build-stempy:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9']
+        mpi: ['ON', 'OFF']
+        ipykernel: ['', 'ipykernel']
+        dev: ['', 'dev']
+        exclude:
+          - MPI: 'ON'
+            ipykernel: 'ipykernel'
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          submodules: 'recursive'
+
+      - name: 'Setup Docker Environment'
+        uses: ./.github/actions/docker_setup
+        with:
+          github_event_name: ${{ github.event_name }}
+          DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+          DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}
+          DOCKERHUB_ORG: ${{ vars.DOCKERHUB_ORG }}
+
+      - name: Determine if Dockerfile.base changed
+        id: changed-dockerfile-base
+        uses: tj-actions/changed-files@v35
+        with:
+          files: |
+            ./docker/Dockerfile.base
+            ./docker/apt-packages-common.txt
+            ./docker/apt-packages-dev.txt
+
+      - name: Set up environment variables for python version
+        id: set-conda-env
+        run: |
+          echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
+          PYTHON_VERSION_NODOT=$(echo ${{ matrix.python-version }} | tr -d .)
+          echo "PYTHON_VERSION_NODOT=${PYTHON_VERSION_NODOT}" >> $GITHUB_ENV
+          - name: Set up other environment variables
+          id: set-tag-vars
+          run: |
+            echo "BASE_TARGET=$(if [[ "${{ matrix.mpi }}" == 'ON' ]]; then 
+              echo 'mpi' 
+            else 
+              echo 'base' 
+            fi)" >> $GITHUB_ENV
+
+            MPI_TAG=$(if [[ "${{ matrix.mpi }}" == 'ON' ]]; then 
+              echo '-mpi' 
+            else 
+              echo '' 
+            fi)
+            echo "MPI_TAG=${MPI_TAG}" >> $GITHUB_ENV
+
+            DEV_TAG=$(if [[ "${{ matrix.dev }}" == 'dev' ]]; then 
+              echo '-dev' 
+            else 
+              echo '' 
+            fi)
+            echo "DEV_TAG=${DEV_TAG}" >> $GITHUB_ENV
+
+            echo "RELEASE_OR_DEBUG=$(if [[ "${{ matrix.dev }}" == 'dev' ]]; then 
+              echo 'Debug' 
+            else 
+              echo 'Release' 
+            fi)" >> $GITHUB_ENV
+
+            COMMIT=$(git rev-parse --short HEAD)
+            echo "COMMIT=${COMMIT}" >> $GITHUB_ENV
+
+            IPYKERNEL_TAG=$(if [[ "${{ matrix.ipykernel }}" == 'ipykernel' ]]; then 
+              echo '-ipykernel' 
+            else 
+              echo '' 
+            fi)
+            echo "IPYKERNEL_TAG=${IPYKERNEL_TAG}" >> $GITHUB_ENV
+
+            BASE_TAG=${{ env.DOCKERHUB_ORG }}/stempy${MPI_TAG}:py${{ env.PYTHON_VERSION_NODOT }}-base${DEV_TAG}
+            echo "BASE_TAG=${BASE_TAG}" >> $GITHUB_ENV
+
+            TAG=${{ env.DOCKERHUB_ORG }}/stempy${MPI_TAG}${IPYKERNEL_TAG}:py${{ env.PYTHON_VERSION_NODOT }}-${COMMIT}${DEV_TAG}
+            echo "TAG=${TAG}" >> $GITHUB_ENV
+
+            LATEST_TAG=${{ env.DOCKERHUB_ORG }}/stempy${MPI_TAG}${IPYKERNEL_TAG}:latest${DEV_TAG}
+            echo "LATEST_TAG=${LATEST_TAG}" >> $GITHUB_ENV
+
+      - name: Build/push Dockerfile.base
+        uses: docker/build-push-action@v3
+        if: ${{ contains(github.event.head_commit.message, 'trigger-ci') || steps.changed-dockerfile-base.outputs.any_changed == 'true'}}
+        with:
+          context: .
+          file: ./docker/Dockerfile.base
+          push: ${{ github.event_name != 'pull_request' }}
+          build-args: |
+            PYTHON_VERSION=${{ env.PYTHON_VERSION }}
+            DEV=${{ matrix.dev }}
+          tags: ${{ env.BASE_TAG }}
+          target: ${{ env.BASE_TARGET }}
+          cache-to: type=gha, mode=max
+          cache-from: type=gha, mode=max
+
+      - name: Build/push Dockerfile.stempy
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          file: ./docker/Dockerfile.stempy
+          push: ${{ github.event_name != 'pull_request' }}
+          build-args: |
+            PYTHON_VERSION=${{ env.PYTHON_VERSION }}
+            BASE_IMAGE=${{ env.BASE_TAG }}
+            RELEASE_OR_DEBUG=${{ env.RELEASE_OR_DEBUG }}
+            MPI=${{ matrix.mpi }}
+            IPYKERNEL=${{ matrix.ipykernel }}
+          tags: |
+            ${{ env.TAG }}
+            ${{ env.LATEST_TAG }}
+          target: build
+          cache-to: type=gha, mode=max
+          cache-from: type=gha, mode=max

docker/Dockerfile.base

@@ -0,0 +1,47 @@
+ARG PYTHON_VERSION
+FROM python:${PYTHON_VERSION} as base
+
+ENV DEBIAN_FRONTEND noninteractive
+WORKDIR /build
+
+# Install common packages
+COPY ./docker/apt-packages-common.txt /tmp/apt-packages-common.txt
+
+# Install dev packages if DEV is set
+COPY ./docker/apt-packages-dev.txt /tmp/apt-packages-dev.txt
+
+ARG DEV
+RUN if [ "$DEV" = "dev" ]; then \
+    cat /tmp/apt-packages-common.txt /tmp/apt-packages-dev.txt > /tmp/apt-packages.txt; \
+    else \
+    cp /tmp/apt-packages-common.txt /tmp/apt-packages.txt; \
+    fi                                                  && \
+    apt-get update                                      && \
+    apt-get upgrade --yes                               && \
+    apt-get install --yes                                  \
+    $(cat /tmp/apt-packages-common.txt)                 && \
+    apt-get clean all                                   && \
+    rm -rf /var/lib/apt/lists/*
+
+FROM base as mpi
+
+# Build mpich
+ARG mpich=4.0.2
+ARG mpich_prefix=mpich-$mpich
+RUN wget https://www.mpich.org/static/downloads/$mpich/$mpich_prefix.tar.gz && \
+    tar xvzf $mpich_prefix.tar.gz -C /build                                 && \
+    rm -rf $mpich_prefix.tar.gz                                             && \
+    cd /build/$mpich_prefix                                                 && \
+    ./configure --disable-f77 --disable-fc --disable-fortran                && \
+    make -j 16                                                              && \
+    make install                                                            && \
+    make clean                                                              && \
+    cd ..                                                                   && \
+    rm -rf $mpich_prefix                                                    
+
+# Build BigMPI
+RUN cd /build && wget https://github.com/jeffhammond/BigMPI/archive/refs/heads/master.tar.gz && \
+    tar zxvf master.tar.gz  && cd /build/BigMPI-master && \
+    ./autogen.sh && ./configure --with-pic && make -j4 && make install && make clean && rm /build/master.tar.gz
+
+RUN /sbin/ldconfig

docker/Dockerfile.stempy

@@ -0,0 +1,34 @@
+ARG BASE_IMAGE
+FROM ${BASE_IMAGE} as build
+
+ENV DEBIAN_FRONTEND noninteractive
+
+ARG PYTHON_VERSION
+ARG IPYKERNEL
+ARG MPI
+ARG RELEASE_OR_DEBUG
+
+COPY . /source/stempy/
+
+RUN pip install -r /source/stempy/requirements.txt
+
+RUN mkdir -p /build/stempy                                                                    && \
+    cd /build/stempy                                                                          && \
+    cmake -DCMAKE_BUILD_TYPE:STRING=${RELEASE_OR_DEBUG} \
+    -Dstempy_ENABLE_VTKm:BOOL=OFF \
+    -Dstempy_ENABLE_MPI:BOOL=${MPI} \
+    -DBIGMPI_INCLUDE_DIR:PATH=/usr/local/include \
+    -DBIGMPI_LIBRARY:PATH=/usr/local/lib/libbigmpi.a \
+    /source/stempy .                                                                          && \
+    make -j 16                                                                                && \
+    cp -r -L /build/stempy/lib/stempy \                                                   
+    /usr/local/lib/python${PYTHON_VERSION}/site-packages                                      
+
+RUN if [ "${IPYKERNEL}" = "ipykernel" ]; then \
+    pip install -r /source/stempy/docker/requirements-ipykernel.txt; \
+    else \
+    pip install -r /source/stempy/docker/requirements-normal.txt; \
+    fi                                                                                        && \
+    rm -rf /source/stempy
+
+RUN /sbin/ldconfig

docker/apt-packages-common.txt

@@ -0,0 +1,20 @@
+apt-transport-https
+autoconf
+automake
+ca-certificates
+gcc
+g++
+git
+gnupg
+libarchive-dev
+libeigen3-dev
+libffi-dev
+libhdf5-dev
+liblapack-dev
+libopenblas-dev
+libsqlite3-dev
+libtool
+make
+software-properties-common
+wget
+zlib1g-dev

docker/apt-packages-dev.txt

@@ -0,0 +1,2 @@
+gdb
+vim

docker/requirements-ipykernel.txt

@@ -0,0 +1,6 @@
+ipykernel=6.4.2
+ipympl=0.8.6
+matplotlib=3.4.3
+click
+imageio
+ncempy

docker/requirements-normal.txt

@@ -0,0 +1,4 @@
+matplotlib
+click
+imageio
+ncempy

requirements.txt

@@ -1,3 +1,4 @@
 numpy
 h5py
 deprecation
+cmake