Merge branch 'bioconda:master' into master #15
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: Upload | |
| on: | |
| push: | |
| branches: | |
| - master | |
| 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@v4 | |
| 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: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| - 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 handle-merged-pr recipes config.yml \ | |
| # --repo bioconda/bioconda-recipes \ | |
| # --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \ | |
| # --quay-upload-target biocontainers \ | |
| # --fallback build | |
| bioconda-utils build recipes config.yml \ | |
| --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \ | |
| --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers | |
| docker rmi quay.io/dpryan79/mulled_container:latest | |
| build-osx-64: | |
| name: OSX-64 Upload | |
| if: github.repository == 'bioconda/bioconda-recipes' | |
| runs-on: macos-13 | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 4 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| 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: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| - 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 | |
| # Sets up OSX SDK | |
| run_conda_forge_build_setup | |
| # bioconda-utils handle-merged-pr recipes config.yml \ | |
| # --repo bioconda/bioconda-recipes \ | |
| # --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \ | |
| # --fallback build | |
| bioconda-utils build recipes config.yml \ | |
| --anaconda-upload --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} | |
| build_and_upload-osx-arm64: | |
| name: OSX-ARM64 Upload | |
| if: github.repository == 'bioconda/bioconda-recipes' | |
| runs-on: macOS-14 # M1 | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 4 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| # bail if there's no osx-arm64 recipes | |
| - name: Check for Additional Platforms | |
| id: additional_platforms | |
| run: | | |
| result=$(./scripts/check-for-additional-platforms.sh "${GITHUB_SHA}~1 ${GITHUB_SHA}" "build_and_upload" "${GITHUB_JOB}") | |
| if [[ ${result} != "build" ]] | |
| then | |
| echo "No recipes using this platform, skipping rest of job." | |
| echo "skip_build=true" >> $GITHUB_OUTPUT | |
| fi | |
| - name: set path | |
| run: | | |
| echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| if: steps.additional_platforms.outputs.skip_build != 'true' | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Set up bioconda-utils | |
| if: steps.additional_platforms.outputs.skip_build != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| - name: Configure conda | |
| if: steps.additional_platforms.outputs.skip_build != 'true' | |
| run: bash configure-conda.sh | |
| - name: Build and Upload | |
| if: steps.additional_platforms.outputs.skip_build != 'true' | |
| 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: ${{ secrets.GITHUB_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "darwin" | |
| CI: "true" | |
| run: | | |
| set -xe | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| source common.sh | |
| # Sets up OSX SDK | |
| run_conda_forge_build_setup | |
| bioconda-utils handle-merged-pr recipes config.yml \ | |
| --repo bioconda/bioconda-recipes \ | |
| --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \ | |
| --fallback build \ | |
| --artifact-source github-actions |