Nightly Uploader #23
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Nightly Uploader | |
| on: | |
| schedule: | |
| - cron: '12 2 * * *' | |
| jobs: | |
| build-linux: | |
| name: Linux Upload | |
| if: github.repository == 'bioconda/bioconda-recipes' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 13 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Restore cache | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }} | |
| - name: Set up bioconda-utils | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| # This has to be done after the cache is restored, because | |
| # the channel setup is not cached as it resides in the home directory. | |
| # We could use a system-wide (and therefore cached) channel setup, | |
| # but mamba does not support that at the time of implementation | |
| # (it ignores settings made with --system). | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and upload | |
| env: | |
| QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }} | |
| QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -ex | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| docker pull quay.io/dpryan79/mulled_container:latest | |
| bioconda-utils build recipes config.yml \ | |
| --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ | |
| --prelint | |
| docker rmi quay.io/dpryan79/mulled_container:latest | |
| build-osx: | |
| name: OSX Tests | |
| if: github.repository == 'bioconda/bioconda-recipes' | |
| runs-on: macOS-latest | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 4 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Restore cache | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }} | |
| - name: Set up bioconda-utils | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| # This has to be done after the cache is restored, because | |
| # the channel setup is not cached as it resides in the home directory. | |
| # We could use a system-wide (and therefore cached) channel setup, | |
| # but mamba does not support that at the time of implementation | |
| # (it ignores settings made with --system). | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and Test | |
| env: | |
| QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }} | |
| QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "darwin" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| # The SDK isn't actually cached, so reinstall it | |
| run_conda_forge_build_setup | |
| bioconda-utils build recipes config.yml \ | |
| --anaconda-upload \ | |
| --prelint |