The WholeCellEcoliRelease repo and the release paper branch

About

The public WholeCellEcoliRelease repository contains a release snapshot of the Covert Lab's Whole Cell Model for Escherichia coli. This is to enable people outside the lab to reproduce the results in the Science paper, to learn from the code, and to tinker with it.

We do not plan to merge Pull Requests into this repository except documentation and installation fixes.

The release-paper branch is a staging area for the WholeCellEcoliRelease repo.

Reproducing its runtime environment gets more difficult over time since Python 2 passed its expiration date, at least one of those pips got yanked from PyPI except in its final version, at least one of those binary libraries now has only a later release on brew for macOS, and Python 3 has many compatibility differences.

To copy changes to the WholeCellEcoliRelease repo

git checkout release-paper
rsync -av --delete --exclude="{.git,.pytest_cache,__pycache__,*.pyc}" wcEcoli/ WholeCellEcoliRelease/

Then review and check in.

Publishing the Docker Image to GitHub Packages

Running a Docker Image is an easier way to bring up the runtime environment. It has its own copy of libraries, executables, Python packages, and the wcEcoli code. It's lighter weight than a Virtual Machine but it's less isolated from the host OS, and neither is isolated from the host CPU model and other hardware details.

How to create and publish the package

cloud/build-containers.sh
docker tag wcm-full:latest docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full:latest
docker push docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full:latest

A few notes about the packages:

• you will need to authenticate in docker to push an image
• images in public repos cannot be deleted (it might be possible under special circumstances for GitHub to take it down)
• GitHub is moving from GitHub Packages to GitHub Container Registry.