Synapse command line CWL tools

This repository contains versioned CWL tools for the Synapse command line client. Other tools that utilize the synapseclient should live in other repositories.

Dockerfile

There is no Dockerfile for this repository, but all tools must use the docker image: sagebionetworks/synapsepythonclient. Whenever there is an update to the synapsePythonClient, these templates should be updated.

CWL

The cwl folder contains tool definitions in the Common Workflow language.

Tests

cwltest is used for testing tools. Tests can be added in tests/test-descriptions.yaml. Tests are automatically performed on pushes in which the most recent commit message does not contain the [skip-ci] string.

Contributing

To contribute changes to the dockerfile or CWL tools, please create a fork of this repository and develop on a feature branch. Pull requests will be reviewed before merging into this repository.

Continuous Deployment and Versioning

This template uses GitHub actions to perform automated versioning, version bumping, building of tagged Docker images, and pushing images to DockerHub.

CI

Defined in .github/workflows/ci.yaml, this action runs on each push to master where the commit does not contain '[skip-ci]'.

Credentials

This uses GitHub secrets to store credentials for the GitHub action to push to the sagebionetworks DockerHub account using a service account. All repositories that are generated from this template will need to have this service account added to it.

Versioning

Versioning is achieved through git tagging using semantic versioning. Each push to master will generate an increment to the patch value, unless the commit contains the string '[skip-ci]'.

The release script has dependencies which can be installed to virtual environment using pipenv. After installing pipenv, run pipenv install to install the dependencies, and pipenv shell to activate the environment.

To do a minor or major release manually:

1. Determine what the tag value will be. For example, to make a minor release from v0.1.22, the next tag would be v0.2.0.
2. In the CWL tools, change the docker version to use that tag, and create a commit like "Update docker version in cwl tools in preparation for minor release"
3. Run the tagging commmand: git tag v0.2.0
4. Push the tag: git push --tags

Branch Versioning

Optionally, you can set up your repository for running the CI action on pushes to all branches, not just master. This is not the default behavior because it introduces complexity and requires that you use git in a certain way.

To set this up, in .github/workflows/ci.yaml, change master to '*' in the event filter ( on > push > branches). This will cause pushes to non-master tags to also build. They will be tagged with this pattern: -, e.g. v1.0.0-197e187.

If you choose to make this change, for best results we recommend that you also use the no-fast-forward flag (--no-ff) when merging branches to master. Using that flag will ensure that a new merge commit is created, and CI will run correctly. Without a new merge commit, versioning won't work correctly.