Added Dockerfile and accessing mdx2 through Docker container

.dockerignore

@@ -0,0 +1,24 @@
+.git
+.github
+.gitignore
+.dockerignore
+.DS_Store
+
+__pycache__
+*.py[cod]
+*.egg-info/
+*.egg
+build/
+dist/
+.eggs/
+
+.env
+.venv
+env/
+venv/
+
+.mypy_cache/
+.pytest_cache/
+.coverage
+htmlcov/
+.ipynb_checkpoints

.github/Dockerfile

@@ -0,0 +1,34 @@
+# diffuseproject/mdx2:1.0.0 (https://hub.docker.com/repository/docker/diffuseproject/mdx2/tags/1.0.0/sha256-abfcf7d2feacdf9a207a13c2bb908d62e6f461259f78e82d3bb8983267446291)
+
+FROM mambaorg/micromamba:1.5.5 AS micromamba_stage
+
+FROM python:3.10-slim AS final
+
+RUN apt-get update && apt-get install -y ca-certificates git
+
+COPY --from=micromamba_stage /bin/micromamba /usr/local/bin/micromamba
+
+ENV PATH="/usr/local/bin:/opt/conda/bin:$PATH"
+ENV JUPYTER_PORT=8888
+
+RUN mkdir -p /opt/conda
+
+WORKDIR /home/dev
+
+COPY env.yaml .
+
+# Use micromamba to create the environment and install packages
+RUN /usr/local/bin/micromamba create -f env.yaml -n mdx2-dev && \
+    /usr/local/bin/micromamba install -y -n mdx2-dev nexpy jupyterlab jupyterlab-h5web dials xia2 wget tar -c conda-forge && \
+    /usr/local/bin/micromamba clean --all --yes
+
+COPY . .
+
+# Install dials-extensions pinned to a specific commit (963fe9e458a505a8443c988d45fb8dcb4532768f) for CHESS beamline compatibility
+# Install the local package in editable mode within the environment
+RUN /usr/local/bin/micromamba run -n mdx2-dev pip install git+https://github.com/FlexXBeamline/dials-extensions.git@963fe9e458a505a8443c988d45fb8dcb4532768f
+RUN /usr/local/bin/micromamba run -n mdx2-dev pip install -e .
+
+EXPOSE 8880-8890
+
+CMD /usr/local/bin/micromamba run -n mdx2-dev jupyter lab --ip=0.0.0.0 --port=$JUPYTER_PORT --no-browser --allow-root

.github/workflows/docker.yml

@@ -0,0 +1,43 @@
+name: docker
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Determine Docker tags
+        id: tags
+        run: |
+          if [ "${{ github.ref }}" = "refs/heads/main" ]; then
+            echo "tags=${{ vars.DOCKERHUB_USERNAME }}/mdx2:latest" >> $GITHUB_OUTPUT
+          else
+            echo "tags=${{ vars.DOCKERHUB_USERNAME }}/mdx2:test" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: .github/Dockerfile
+          push: ${{ github.ref == 'refs/heads/main' }}
+          tags: ${{ steps.tags.outputs.tags }}

README.md

@@ -44,7 +44,7 @@ Publications describing [ando-lab/mdx2](https://github.com/ando-lab/mdx2):
 
 ### Prerequisites
 
-For a conda-based installation, you'll need [micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) or equivalent.
+For a conda-based installation, you'll need [micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) or equivalent. The Docker-based installation requires you to install and login to [Docker](https://www.docker.com/get-started/).
 
 ### User install (conda environment)
 
@@ -71,3 +71,24 @@ pip install -e ".[dev]"
 ```
 
 The last line installs mdx2 in editable mode, with optional development tools including pytest and ruff
+
+### Developer Install (Docker container)
+
+Pull image from Docker Hub and run the container. Search the Docker container logs for the localhost address to access mdx2 within a Jupyter Lab notebook or terminal.
+
+- Docker image exposes ports 8880-8890 (default: 8888)
+- Platform: linux/amd64
+```bash
+git clone https://github.com/diff-use/mdx2.git
+cd mdx2
+docker pull diffuseproject/mdx2:1.0.0
+docker run --platform linux/amd64 --name mdx2_container -it -d -e JUPYTER_PORT={CONTAINER_PORT} -p {HOST_PORT}:{CONTAINER_PORT} -v "$(pwd)":/home/dev diffuseproject/mdx2:1.0.0
+docker logs mdx2_container
+```
+
+(Optional) Open a shell in the running container:
+```bash
+docker exec -it mdx2_container /bin/bash
+eval "$(micromamba shell hook --shell bash)"
+micromamba activate 'mdx2-dev'
+```