diff --git a/.github/workflows/canvas-upload.yml b/.github/workflows/canvas-upload.yml index 3630b88d..8ceecc00 100644 --- a/.github/workflows/canvas-upload.yml +++ b/.github/workflows/canvas-upload.yml @@ -1,4 +1,4 @@ -name: canvas-upload +name: Canvas upload on: workflow_dispatch: @@ -6,22 +6,25 @@ on: - main - devel push: - paths: - - 'pages/tools-for-reproducible-research.md' - - 'pages/upload-page-to-canvas.sh' branches: - main - devel + paths: + - 'pages/tools-for-reproducible-research.md' + - 'pages/upload-page-to-canvas.sh' + jobs: upload: runs-on: ubuntu-latest container: pandoc/latex steps: - - uses: actions/checkout@v2 - with: - fetch-depth: 0 - - name: Upload pages - env: - API_TOKEN: ${{ secrets.CANVAS_API_TOKEN }} - run: | - bash pages/upload-page-to-canvas.sh pages/tools-for-reproducible-research.md $API_TOKEN + - name: Checkout + uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Upload landing page to Canvas + env: + API_TOKEN: ${{ secrets.CANVAS_API_TOKEN }} + run: | + bash pages/upload-page-to-canvas.sh pages/tools-for-reproducible-research.md $API_TOKEN diff --git a/.github/workflows/docker-run.yml b/.github/workflows/docker-run.yml index 15386c86..087157f8 100644 --- a/.github/workflows/docker-run.yml +++ b/.github/workflows/docker-run.yml @@ -19,8 +19,10 @@ jobs: docker-build-and-run: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - name: Checkout + uses: actions/checkout@v4 + - name: Docker build run: | docker build -t my_docker_project -f tutorials/containers/Dockerfile tutorials/containers/ - docker run --rm my_docker_project \ No newline at end of file + docker run --rm my_docker_project diff --git a/.github/workflows/setup.yml b/.github/workflows/setup.yml index b84ec5a7..83cf15dd 100644 --- a/.github/workflows/setup.yml +++ b/.github/workflows/setup.yml @@ -8,13 +8,14 @@ on: pull_request: branches: - main + - devel jobs: install: runs-on: ${{ matrix.os }} strategy: matrix: - os: [ macos-latest, ubuntu-latest ] + os: [macos-latest, ubuntu-latest] env: [snakemake, nextflow, jupyter, quarto] include: - env: snakemake @@ -26,16 +27,18 @@ jobs: - env: quarto cmd: mamba install -c conda-forge quarto && mamba install -c conda-forge deno && export QUARTO_DENO=$(which deno) && quarto render tutorials/quarto/quarto-tutorial-example.qmd --to html steps: - - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2.2.0 + - name: Checkout + uses: actions/checkout@v4 + + - name: Conda setup + uses: conda-incubator/setup-miniconda@v3 with: - miniforge-variant: Mambaforge miniforge-version: latest activate-environment: ${{ matrix.env }}-env environment-file: tutorials/${{ matrix.env }}/environment.yml - use-mamba: true channel-priority: strict - - name: Test ${{ matrix.env }} + + - name: Test ${{ matrix.env }} Conda environment shell: bash -l {0} run: | conda list