correct testing calls for GitHub Actions in Docker containers

    - name: Diagnostics

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls

  test:

  call:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2

        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Run image

      run: docker run docker.pkg.github.com/minoda-lab/universc/universc:latest echo "hello from universc"

    - name: Call UniverSC

    - name: Run image test

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello from universc"

    - name: Call UniverSC test

      uses: addnab/docker-run-action@v1

      with:

        image: tomkellygenetics/universc:latest

        run: bash /universc/test/test_call.sh

    - name: Run image

      run: docker run docker.pkg.github.com/minoda-lab/universc/universc:latest bash /universc/test/run_tests_10x.sh

    - name: Call UniverSC

        run: echo "hello from universc"

    - name: Call UniverSC from image

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x.sh

    - name: Call UniverSC from container

      uses: addnab/docker-run-action@v1

      with:

        image: tomkellygenetics/universc:latest

name: Render-Webpages

# Run this workflow every time a new commit pushed to your repository (includes merged PR)

on: push

jobs:

  # Set the job key. The key is displayed as the job name

  # when a job name is not provided

  build-webpages:

    # Name the Job

    name: Update lessons

    # Set the type of machine to run on

    runs-on: tomkellygenetics/cellranger_clean:3.0.2.9001

    strategy:

      matrix:

        lesson-repo: [shell-novice, git-novice, r-novice-gapminder]

        ##lesson-repo: [shell-novice, git-novice, r-novice-gapminder, r-novice-inflammation, python-novice-gapminder, python-novice-inflammation, sql-novice-survey, make-novice]

        python-version: [3.7]

    steps:

      # Checks out a copy of your repository on the ubuntu-latest machine

      - name: Checkout code

        uses: actions/checkout@v2

      - uses: actions/checkout@v2

      - name: Set up Python ${{ matrix.python-version }}

        uses: actions/setup-python@v2

        with:

          python-version: ${{ matrix.python-version }}

      - name: install shell dependencies

        run: sudo apt-get install -y git

      - name: update python package manager

        run: pip install --upgrade pip

      - name: install python dependencies

        run: pip install python-dateutil 

      - name: where am i

        run: pwd

      - name: list files

        run: ls

      - name: list parent files

        run: ls ..

      - name: configure git access

        run: export GITHUB_TOKEN=${{ secrets.ACTIONS_TOKEN }}

      - name: configure git account

        run: git config --global user.email "tomkellygenetics@gmail.com"

      - name: configure git user

        run: git config --global user.name "TomKellyGenetics"

      - name: configure git settings

        run: git config --global pull.rebase false 

      - name: who am i

        run: git config -l | cat 

      - name: Build ${{ matrix.lesson-repo }} lesson

        run: bash wrapper.sh --repo ${{ matrix.lesson-repo }} --locale ja --account swcarpentry-ja --webpages

        env:

          DEFAULT_BRANCH: ja

          GITHUB_TOKEN: ${{ secrets.ACTIONS_TOKEN }}

name: Super-Linter

# Run this workflow every time a new commit pushed to your repository (includes merged PR)

on: push

on: workflow_dispatch

jobs:

  # Set the job key. The key is displayed as the job name