pytest workflow (StanfordAHA/garnet)

The pytest workflow from StanfordAHA/garnet, explained and optimized by Latchkey.

CI health: C - fair

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Source: StanfordAHA/garnet.github/workflows/pytest.ymlLicense BSD-3-ClauseView source

What it does

This is the pytest workflow from the StanfordAHA/garnet repository, a real project running GitHub Actions. It is shown here with attribution under its BSD-3-Clause license.

Below, Latchkey shows a faster, safer version produced by its optimization engine.

The workflow

workflow (.yml)

name: pytest

on:
  # Every push
  push:

  # When requested manually
  workflow_dispatch:

  # Every morning at 3am -- how does it know which branch to run??
  schedule:
  - cron: '0 3 * * *'


jobs:
  build:

    runs-on: ubuntu-latest
    if: "!contains(github.event.head_commit.message, 'skip ci')"

    steps:
    - uses: actions/checkout@v6

    - name: Checkout submodules
      shell: bash
      run: |
        git submodule sync --recursive
        git submodule update --init --force --recursive --depth=1

    - name: Pull and run docker
      shell: bash
      run: |
        docker pull stanfordaha/garnet:latest
        docker run -d -it --name CONTAINER stanfordaha/garnet:latest bash
        docker exec CONTAINER /bin/bash -c "rm -rf /aha/garnet"
        docker exec CONTAINER /bin/bash -c "source /aha/bin/activate; pip install psutil"
        docker cp ../garnet CONTAINER:/aha/garnet

    - name: Run tests
      shell: bash
      run: |
        docker exec -i CONTAINER bash -c "/aha/garnet/.github/scripts/run_pytest.sh"

    - name: Upload Coverage
      shell: bash
      # CODECOV_TOKEN secret stored at https://github.com/StanfordAHA/garnet/settings/secrets/actions
      run: |
        docker exec -i CONTAINER bash -c "cd /aha/garnet/ && bash <(curl -s https://codecov.io/bash) -t ${{ secrets.CODECOV_TOKEN }}"

The same workflow, on Latchkey

Removes redundant runs and caps runaway jobs. Added and changed lines are highlighted.

name: pytest
 
on:
  # Every push
  push:
 
  # When requested manually
  workflow_dispatch:
 
  # Every morning at 3am -- how does it know which branch to run??
  schedule:
  - cron: '0 3 * * *'
 
 
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true
 
jobs:
  build:
    timeout-minutes: 30
 
    runs-on: latchkey-small
    if: "!contains(github.event.head_commit.message, 'skip ci')"
 
    steps:
    - uses: actions/checkout@v6
 
    - name: Checkout submodules
      shell: bash
      run: |
        git submodule sync --recursive
        git submodule update --init --force --recursive --depth=1
 
    - name: Pull and run docker
      shell: bash
      run: |
        docker pull stanfordaha/garnet:latest
        docker run -d -it --name CONTAINER stanfordaha/garnet:latest bash
        docker exec CONTAINER /bin/bash -c "rm -rf /aha/garnet"
        docker exec CONTAINER /bin/bash -c "source /aha/bin/activate; pip install psutil"
        docker cp ../garnet CONTAINER:/aha/garnet
 
    - name: Run tests
      shell: bash
      run: |
        docker exec -i CONTAINER bash -c "/aha/garnet/.github/scripts/run_pytest.sh"
 
    - name: Upload Coverage
      shell: bash
      # CODECOV_TOKEN secret stored at https://github.com/StanfordAHA/garnet/settings/secrets/actions
      run: |
        docker exec -i CONTAINER bash -c "cd /aha/garnet/ && bash <(curl -s https://codecov.io/bash) -t ${{ secrets.CODECOV_TOKEN }}"

What changed

Run on Latchkey managed runners with one line (runs-on), which apply the fixes below automatically and self-heal transient failures. This example uses latchkey-small; pick the runner size that fits the job.
Cancel superseded runs when a branch or PR gets a newer push.
Add a job timeout so a hung step cannot burn hours of runner time.

What Latchkey heals here

This workflow has steps that commonly fail on transient issues (network, registries, flaky browsers). On Latchkey managed runners they are detected, retried, and self-healed instead of failing your build:

Dependency installs
Container pulls and builds

This workflow runs 1 job per trigger. On Latchkey the same minutes cost up to 58% less than GitHub-hosted, with zero queue time.

Actions used in this workflow

actions/checkout