Actions

A collection of reusable github actions for facilitating CI/CD at MyOme.

How to use
Docker workflows
Python workflows

How to use

In your .github/workflows directory, create a yaml file (such as main.yaml). Add a job for each desired workflow with the uses keyword. Use the with keyword to pass any desired variables.

Example:

on: [push]

jobs:
  lint:
    uses: myome/actions/.github/workflows/pylint.yaml@main
    with:
      src: "src"
  black:
    uses: myome/actions/.github/workflows/black.yaml@main
    with:
      src: "src"
      py-version: "3.9"

Docker

build-and-push-to-shr-ecr:

 Inputs
 dockerfile: dockerfile to build (defaults to "Dockerfile")
 build_context: build context for docker build command (defaults to ".")

 Secrets
 aws-access-key-id: SHR_ECR_CI_ACCESS_KEY_ID as stored in secrets manager
 aws-secret-access-key: SHR_ECR_CI_SECRET_ACCESS_KEY as stored in secrets manager

Nextflow

nextflow-smoke-test:

 Inputs
 config: Workflow config file (defaults to "workflow/nextflow_smoke_test.config")
 entry: Entry point for specific workflow (defaults to "command_line")

 Secrets
 aws-access-key-id: SHR_S3_FLOWS_CI_ACCESS_KEY_ID as stored in secrets manager
 aws-secret-access-key: SHR_S3_FLOWS_CI_SECRET_ACCESS_KEY as stored in secrets manager

tag-and-ship-nf-workflow:

 Inputs
 bucket: AWS s3 bucket to ship workflow to (defaults to "myome-shr-flows")
 region: AWS region where target bucket exists (defaults to "us-east-2")

 Secrets
 aws-access-key-id: SHR_S3_FLOWS_CI_ACCESS_KEY_ID as stored in secrets manager
 aws-secret-access-key: SHR_S3_FLOWS_CI_SECRET_ACCESS_KEY as stored in secrets manager

Python

bandit: code security checks

 Inputs
 src: source directory (defaults to ".")
 options: bandit flags (defaults to "-r")
 py-version: version of python to use (defaults to "3.x")

black: code formatting

 Inputs
 src: source directory (defaults to ".")
 options: black flags
 py-version: version of python to use (defaults to "3.x")

flake8: style guide enforcement

 Inputs
 src: source directory (defaults to ".")
 options: flake8 flags

mypy: static type checking

 Inputs
 src: source directory (defaults to ".")
 options: mypy flags (defaults to "-v")

publish: upload packages to Myome SHR pypi

 Inputs
 py-version: version of python to use (defaults to "3.x")

 Secrets
 pypi-pw: SHR_PYPI_CICD_UPLOAD_PWD stored as Github secret

pylint: static code analysis

 Inputs
 src: source directory (defaults to ".")
 options: pylint flags

pytest: test code runner

 Inputs
 src: source directory (defaults to ".")
 options: pytest flags (defaults to "-v")

References

• https://docs.github.com/en/actions/learn-github-actions/reusing-workflows
• https://bandit.readthedocs.io/en/latest/
• https://black.readthedocs.io/en/stable/
• https://flake8.pycqa.org/en/latest/
• https://mypy.readthedocs.io/en/stable/
• https://pylint.org/
• https://docs.pytest.org/