Docker dev setup

Dockerfile

@@ -60,12 +60,30 @@ RUN conda config --set ssl_verify false && \
     conda config --set ssl_verify true
 
 # Step 5: Make the environment available (simulate "conda activate spac")
+# Set all necessary environment variables for conda activation
 ENV CONDA_DEFAULT_ENV=${ENV_NAME}
+ENV CONDA_PREFIX=/opt/conda/envs/${ENV_NAME}
 ENV PATH=/opt/conda/envs/${ENV_NAME}/bin:${PATH}
+ENV PYTHONPATH=/opt/conda/envs/${ENV_NAME}/lib/python3.9/site-packages:${PYTHONPATH}
 
 # Step 6: "Install the SPAC package in development mode"
 RUN /opt/conda/envs/${ENV_NAME}/bin/pip install -e .
 
+# Make conda activate spac environment automatically in bash shells
+RUN echo "source /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate ${ENV_NAME}" >> ~/.bashrc
+
+# Create a wrapper script that ensures conda environment is activated
+# This helps when Galaxy runs commands directly
+RUN echo '#!/bin/bash' > /usr/local/bin/conda-run && \
+    echo 'source /opt/conda/etc/profile.d/conda.sh' >> /usr/local/bin/conda-run && \
+    echo 'conda activate spac' >> /usr/local/bin/conda-run && \
+    echo 'exec "$@"' >> /usr/local/bin/conda-run && \
+    chmod +x /usr/local/bin/conda-run
+
+# Set the shell to use bash for RUN commands
+SHELL ["/bin/bash", "-c"]
+
 # Set environment variables for headless notebook execution
 ENV QT_QPA_PLATFORM=offscreen
 ENV MPLBACKEND=Agg
@@ -76,13 +94,21 @@ RUN mkdir -p /workspace /data /results
 # Install jupyter and nbconvert for notebook testing
 RUN /opt/conda/envs/${ENV_NAME}/bin/pip install jupyter nbconvert
 
-# Verify SPAC installation works correctly
+# Verify SPAC installation works correctly in multiple ways
 RUN echo "=== VERIFYING SPAC INSTALLATION ===" && \
-    /opt/conda/envs/${ENV_NAME}/bin/python -c "import spac; print(f'SPAC version: {spac.__version__}'); import scimap; print('All modules imported successfully!')" || \
-    echo "Some import issues detected but proceeding with test"
+    echo "Test 1: Direct python call" && \
+    python -c "import spac; print(f'SPAC version: {spac.__version__}')" && \
+    echo "Test 2: Which python" && \
+    which python && \
+    echo "Test 3: Python path" && \
+    python -c "import sys; print(sys.executable)" && \
+    echo "Test 4: Import scimap" && \
+    python -c "import scimap; print('scimap imported successfully')" && \
+    echo "=== ALL TESTS PASSED ===" || \
+    echo "Some import issues detected but proceeding"
 
 # Set working directory for Jupyter (will be mounted via volume)
 WORKDIR /workspace
 
 # Default command starts Jupyter notebook server
-CMD ["/opt/conda/envs/spac/bin/jupyter", "notebook", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token=", "--NotebookApp.password="]
+CMD ["/opt/conda/envs/spac/bin/jupyter", "notebook", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token=", "--NotebookApp.password="]

Makefile

@@ -0,0 +1,87 @@
+.PHONY: help build run dev stop clean rebuild test
+
+# Default target
+help:
+	@echo "SPAC Docker Management"
+	@echo "======================"
+	@echo ""
+	@echo "Production targets:"
+	@echo "  make build          - Build production Docker image"
+	@echo "  make run            - Run production container with Jupyter"
+	@echo "  make test           - Run tests in production container"
+	@echo ""
+	@echo "Development targets:"
+	@echo "  make dev            - Start development environment with live code mounting"
+	@echo "  make dev-bash       - Start development container with bash shell"
+	@echo "  make dev-test       - Run tests in development mode"
+	@echo ""
+	@echo "Utility targets:"
+	@echo "  make stop           - Stop all running containers"
+	@echo "  make clean          - Remove containers and images"
+	@echo "  make rebuild        - Clean and rebuild production image"
+	@echo "  make logs           - Show container logs"
+
+# Production build
+build:
+	@echo "Building production Docker image..."
+	docker build -t spac:latest .
+
+# Run production container
+run:
+	@echo "Starting production container with Jupyter..."
+	docker run -d \
+		--name spac-prod \
+		-p 8888:8888 \
+		-v $(PWD)/data:/data \
+		-v $(PWD)/results:/results \
+		spac:latest
+	@echo "Jupyter available at http://localhost:8888"
+
+# Development environment with live code mounting
+dev:
+	@echo "Starting development environment with live code mounting..."
+	docker-compose -f docker/docker-compose.dev.yml up -d
+	@echo "Development Jupyter available at http://localhost:8889"
+	@echo "Source code is mounted - changes will be reflected immediately!"
+
+# Development with bash shell
+dev-bash:
+	@echo "Starting development container with bash shell..."
+	docker-compose -f docker/docker-compose.dev.yml run --rm --service-ports spac-dev bash
+
+# Run tests in development mode
+dev-test:
+	@echo "Running tests in development mode..."
+	docker-compose -f docker/docker-compose.dev.yml run --rm spac-dev \
+		/opt/conda/envs/spac/bin/pytest tests/ -v
+
+# Run tests in production container
+test:
+	@echo "Running tests in production container..."
+	docker run --rm spac:latest \
+		/opt/conda/envs/spac/bin/pytest tests/ -v
+
+# Stop all containers
+stop:
+	@echo "Stopping containers..."
+	-docker stop spac-prod 2>/dev/null || true
+	-docker-compose -f docker/docker-compose.dev.yml down 2>/dev/null || true
+
+# Clean up containers and images
+clean: stop
+	@echo "Cleaning up containers and images..."
+	-docker rm spac-prod 2>/dev/null || true
+	-docker rmi spac:latest 2>/dev/null || true
+	-docker-compose -f docker/docker-compose.dev.yml down -v 2>/dev/null || true
+
+# Rebuild from scratch
+rebuild: clean build
+	@echo "Rebuild complete!"
+
+# Show logs
+logs:
+	@echo "=== Production logs ==="
+	-docker logs spac-prod 2>/dev/null || echo "No production container running"
+	@echo ""
+	@echo "=== Development logs ==="
+	-docker-compose -f docker/docker-compose.dev.yml logs 2>/dev/null || echo "No development container running"

README.md

@@ -38,7 +38,14 @@ conda config --set ssl_verify true
 
 ## Using SPAC with Docker
 
-For a reproducible environment, you can use Docker to run SPAC:
+For a reproducible environment, you can use Docker to run SPAC.
+
+**📘 For detailed Docker documentation including development mode with live code mounting, see [`docker/README.md`](docker/README.md)**
+
+**Quick commands:**
+- Production: `make build` → `make run`
+- Development: `make dev` (changes to `src/` reflected immediately!)
+- Help: `make help`
 
 ### Build the Docker Image
 ```bash

docker/Dockerfile.dev

@@ -0,0 +1,98 @@
+FROM continuumio/miniconda3:24.3.0-0
+
+# Build arguments
+ARG ENV_NAME=spac
+
+# Set labels
+LABEL maintainer="FNLCR-DMAP"
+LABEL description="SPAC - Single Cell Spatial Analysis Container (Development)"
+LABEL version="0.9.0-dev"
+
+# Install system dependencies including Chromium for Kaleido (ARM64 compatible)
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    git \
+    ca-certificates \
+    build-essential \
+    libgl1-mesa-glx \
+    libglib2.0-0 \
+    libsm6 \
+    libxext6 \
+    libxrender-dev \
+    libgomp1 \
+    libglu1-mesa \
+    xvfb \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Chromium for Kaleido visualization support (ARM64 compatible)
+RUN apt-get update && \
+    apt-get install -y chromium && \
+    rm -rf /var/lib/apt/lists/*
+
+# Set Chrome binary path for Kaleido
+ENV CHROME_BIN=/usr/bin/chromium
+
+# Install and configure libmamba solver
+RUN conda install -n base -y conda-libmamba-solver && \
+    conda config --set solver libmamba
+
+# Set up working directory
+WORKDIR /home/reviewer/SCSAWorkflow
+
+# Copy only environment setup files first (for better layer caching)
+COPY environment.yml .
+
+# Configure conda channels
+RUN conda config --add channels https://fnlcr-dmap.github.io/scimap/ && \
+    conda config --add channels conda-forge && \
+    conda config --add channels ohsu-comp-bio && \
+    conda config --add channels leej3 && \
+    conda config --add channels bioconda
+
+# Create the Conda environment
+RUN conda config --set ssl_verify false && \
+    conda env create -f environment.yml && \
+    conda clean -afy && \
+    conda config --set ssl_verify true
+
+# Make the environment available
+ENV CONDA_DEFAULT_ENV=${ENV_NAME}
+ENV PATH=/opt/conda/envs/${ENV_NAME}/bin:${PATH}
+
+# Make conda activate spac environment automatically in bash shells
+RUN echo "source /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate ${ENV_NAME}" >> ~/.bashrc
+
+# Copy setup.py and other necessary files for package installation
+COPY setup.py .
+COPY LICENSE .
+COPY README.md .
+COPY CHANGELOG.md .
+
+# Create a minimal src directory structure for initial installation
+# The actual source code will be mounted as a volume
+RUN mkdir -p src/spac && \
+    touch src/spac/__init__.py
+
+# Install the SPAC package in editable mode
+# The source code will be mounted, so changes will be reflected
+RUN /opt/conda/envs/${ENV_NAME}/bin/pip install -e .
+
+# Set environment variables for headless execution
+ENV QT_QPA_PLATFORM=offscreen
+ENV MPLBACKEND=Agg
+
+# Create working directories
+RUN mkdir -p /workspace /data /results
+
+# Install jupyter and nbconvert for notebook testing
+RUN /opt/conda/envs/${ENV_NAME}/bin/pip install jupyter nbconvert
+
+# Install development tools
+RUN /opt/conda/envs/${ENV_NAME}/bin/pip install ipdb pytest-watch black flake8 isort
+
+# Set working directory for Jupyter
+WORKDIR /workspace
+
+# Default command starts Jupyter notebook server
+CMD ["/opt/conda/envs/spac/bin/jupyter", "notebook", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token=", "--NotebookApp.password="]