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HuBMAP pipeline release management

Overview

This package provides a convenience script which automates some aspects of tagging and releasing production-ready versions of HuBMAP computational analysis pipelines.

Installation

Run python3 -m pip install hubmap-pipeline-release-mgmt.

Usage

Once the package is installed, navigate to a repository containing a pipeline, and ensure that the main branch is what you would like to release as a new tagged version, including the committed state of any submodules. (See Configuration for setting persistent configuration parameters globally or for each pipeline, including the name of the "main" branch.)

Choose a new version number (preferably starting with v), like v1.0, and run:

tag_release_pipeline v1.0

Most of the script is automated, but Git will ask you for a tag message (by opening a text editor) unless a tag message is given as an argument to this script via the --tag-message argument.

To sign Git tags with GPG, append --sign (and if you want to sign with a non-default key, add --sign=preferred@email.address).

(Your local main branch can be behind or ahead of its remote version -- if behind, it will be updated with git pull, and if ahead the remote branch will be updated with git push. Your main branch and its remote version cannot have diverged, however; tag_release_pipeline will abort if this is the case.)

The tag_release_pipeline script makes several assumptions about the state of your repository, and if these assumptions are violated, the script will probably fail loudly and leave your local copy in an arbitrary state. Make sure you have no local modifications for best results (though you shouldn't anyway, if preparing a release version of a pipeline).

At a high level, tag_release_pipeline does:

  • Checkout the main branch, pull/push so it and its remote version match
  • Checkout or create a release branch, git pull --ff-only if checking out a local branch that already exists
  • Sync the main branch to the release branch -- note that this is not a merge; the previous contents of the release branch are overwritten entirely
  • Update the content of all submodules to match the versions committed in the main branch
  • Build all Docker images in docker_images.txt, using the multi-docker-build package
  • Tag all images as latest and with the new tag name
  • Push all Docker images/tags to Docker Hub
  • Update all CWL files to use tagged versions of any images built from the pipeline repository (i.e. those listed in docker_images.txt)
  • Commit the updated CWL files (on the release branch)
  • Tag the new commit, signed or not
  • Push the main and release branches, and the new tag

Options:

--pretend Don't run anything that would make any modifications to any Git repositories or Docker images. This will still run git branch -a to obtain the list of Git branches, however. This will print all commands which would be run.
--tag-message (alias: -m) Use this string as the tag message. This is given to Git as the -m argument to git tag, which stops Git from asking for a tag message interactively.
--sign Sign the new tag with GPG using your default identity.
--sign=identity
 Sign the new tag with GPG, using the specified identity (email address).
--no-push Don't push anything to Docker Hub or the Git remote repository. Everything will be committed, tagged, and built locally.
--main-branch Name of the main branch. Overrides the default (master) and anything found in configuration files.
--release-branch
 Name of the release branch. Overrides the default (release) and anything found in configuration files.
--remote-repository
 Name of the remote repository. Overrides the default (origin) and anything found in configuration files.

Configuration

This package uses the confuse library to read user and pipeline configuration. The default configuration specifies branch names, the remote repository name, and whether to sign each release version of a pipeline, via the following contents of config_default.yaml:

main_branch: master
release_branch: release
remote_repository: origin
sign: false

This configuration can be overridden globally (affecting all usage of this package) and separately for each repository. These configuration parameters are read in this order, with each source overriding earlier ones:

  1. Package default configuration shown above
  2. Global (user) configuration from ~/.config/hubmap_pipeline_release_mgmt/config.yaml (on Linux)
  3. Pipeline configuration options, from pipeline_release_mgmt.yaml in the base directory of the pipeline repository
  4. Command-line arguments passed to the tag_release_pipeline script

For example, to sign all Git tags by default with a specific GPG key, you could create the user configuration file noted above, containing:

sign: mruffalo@cs.cmu.edu

The default main_branch of master is likely to change in the near future.

Requirements

Python 3.6 or newer.

The following package dependencies should be automatically installed when installing via pip or python setup.py install:

  • Version 0.7.1 or newer of the multi-docker-build PyPI package
  • confuse, (recent) version unimportant