Update container infrastructure

[lispandfound]

Updates the container build pipeline to reflect my recent usage of the infrastructure. The idea is to separate the two containers into:

1. A bootstrap container that contains a pre-baked install of everything except EMOD3D which we can't publish.
2. A minimal runner.def that takes the last step of installing EMOD3D.

Then a simple flow.cylc workflow stage can actually produce the runner.sif file immediately like so

[[build_container]]
script = """
git clone --depth 1 git@github.com:ucgmsim/EMOD3D.git
cp ${CYLC_WORKFLOW_RUN_DIR}/runner.def .
apptainer build runner.sif runner.def
mv runner.sif ${CYLC_WORKFLOW_RUN_DIR}
"""

the main advantage of this is that the entire workflow is self-contained and we do not have to shuttle around large runner.sif files.

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request refactors the container infrastructure to optimize the build process for EMOD3D. By introducing a two-stage approach with a pre-built bootstrap container and a minimal runner definition, the changes aim to create a more efficient and self-contained workflow for generating the final runner.sif image, reducing dependencies and simplifying deployment.

Highlights

• Container Infrastructure Separation: The container build process has been refactored into two distinct stages: a bootstrap container and a minimal runner definition, enhancing modularity and efficiency.
• New Bootstrap Dockerfile: A new container/Dockerfile was added to create a base image containing pre-installed common dependencies like build tools, Python 3.13.1, and Rust, excluding EMOD3D.
• Streamlined Runner Definition: The container/runner.def was updated to leverage the new bootstrap image, simplifying its role to primarily focus on the final EMOD3D installation and compilation.
• Self-Contained Workflow: This new two-stage approach enables a more self-contained workflow for building runner.sif files directly within a Cylc workflow stage, eliminating the need to transfer large intermediate files.

Changelog

• container/Dockerfile
  • Added a new Dockerfile to create a base image with core dependencies.
  • Configured Python 3.13.1 installation from source.
  • Included Rust installation and virtual environment setup.
• container/runner.def
  • Modified to use the new earthquakesuc/workflow-bootstrap:latest image as its base.
  • Simplified the %post section to only compile EMOD3D, removing redundant dependency installations and data downloads.
  • Updated environment variables to reflect the new software paths from the bootstrap image.

Ignored Files

• Ignored by pattern: .github/workflows/** (1)
  • .github/workflows/container.yml

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[gemini-code-assist]

Code Review

This pull request refactors the container build process by splitting it into a bootstrap Docker image and a minimal Apptainer runner definition. This is a good approach to streamline the workflow. My review focuses on improving the reproducibility of the builds and fixing a critical issue where compiled binaries were being deleted.

Key feedback points:

• Pinning base image versions in both the Dockerfile and runner.def to ensure reproducible builds.
• Correcting a critical bug in runner.def where compiled binaries were removed during a cleanup step.
• A minor cleanup in an environment variable definition.

[Copilot]

Pull request overview

Updates the container build approach to split “bootstrap” dependencies into a publishable Docker image, and keep the private EMOD3D install/build step in a lightweight Apptainer runner.def, enabling self-contained workflow runs without distributing large .sif artifacts.

Changes:

• Refactors container/runner.def to build EMOD3D on top of a prebuilt bootstrap image.
• Adds a new container/Dockerfile to build the publishable bootstrap Docker image (toolchain, Python, Rust, workflow install).
• Replaces the GitHub Actions workflow to build/push the Docker image and run tests via docker run instead of building/uploading an Apptainer image.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 8 comments.

File	Description
container/runner.def	Switches Apptainer base to a prebuilt bootstrap image and builds EMOD3D from a provided source directory.
container/Dockerfile	Introduces a bootstrap Docker image build (system deps, Python from source, Rust, venv, installs workflow).
.github/workflows/container.yml	Updates CI to build/push the bootstrap Docker image to Docker Hub and run pytest in a container.

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