Update muscle to 5.3 #1974
Workflow file for this run
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: PR Check | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| concurrency: | |
| group: build-${{ github.event.pull_request.number || github.head_ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 13 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Perform lint | |
| env: | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| source common.sh | |
| echo '============' | |
| conda info --all | |
| conda config --show-sources | |
| python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' | |
| echo '============' | |
| if [ -z "$GITHUB_BASE_REF" ] ; then | |
| export GITHUB_BASE_REF="master" | |
| fi | |
| git fetch origin "$GITHUB_BASE_REF" | |
| bioconda-utils lint --loglevel debug --full-report --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| conda clean -y --all | |
| build-linux: | |
| name: Linux Tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 13 | |
| needs: lint | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and test | |
| env: | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -e | |
| # Clean up lingering build artifacts | |
| for n in linux-64 osx-64 noarch; do | |
| rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2 | |
| rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.conda | |
| done | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| source common.sh | |
| if [ -z "$GITHUB_BASE_REF" ] ; then | |
| export GITHUB_BASE_REF="master" | |
| fi | |
| git fetch origin "$GITHUB_BASE_REF" | |
| bioconda-utils build recipes config.yml \ | |
| --docker --mulled-test \ | |
| --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| - name: Prepare artifacts | |
| run: | | |
| ( | |
| rm -rf /tmp/artifacts | |
| mkdir -p /tmp/artifacts/packages | |
| cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
| find -name .cache | xargs rm -rf || true | |
| for n in index.html channeldata.json linux-64 osx-64 noarch; do | |
| cp -rv $n /tmp/artifacts/packages || true | |
| done | |
| if command -V docker >/dev/null; then | |
| mkdir -p /tmp/artifacts/images | |
| cd /tmp/artifacts/images | |
| docker image ls --format='{{.Repository}}:{{.Tag}}' | \ | |
| { grep biocontainers || true ; } | \ | |
| xargs -n1 -P4 bash -c ' | |
| test -n "${1+x}" || exit 0 | |
| echo "Start compressing docker image ${1} ..." | |
| docker save "${1}" | gzip -c > "${1##*/}.tar.gz" | |
| echo "Finished compressing docker image ${1} ." | |
| ' -- | |
| # There's no : allowed in artifact names, replace it with --- | |
| for f in /tmp/artifacts/images/*:* ; do mv -- "$f" "${f//:/---}"; done | |
| fi | |
| ) || true | |
| - name: Archive packages | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: linux-packages | |
| path: | | |
| /tmp/artifacts | |
| build-osx-64: | |
| name: OSX-64 Tests | |
| runs-on: macos-13 | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 4 | |
| # Limited concurrency for osx, so first make sure linux can pass | |
| needs: build-linux | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and Test | |
| env: | |
| # Mimic circleci | |
| OSTYPE: "darwin" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| source common.sh | |
| # Sets up OSX SDK | |
| run_conda_forge_build_setup | |
| # Clean up lingering build artifacts | |
| for n in linux-64 osx-64 noarch; do | |
| rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2 | |
| done | |
| if [ -z "$GITHUB_BASE_REF" ] ; then | |
| export GITHUB_BASE_REF="master" | |
| fi | |
| git fetch origin "$GITHUB_BASE_REF" | |
| bioconda-utils build recipes config.yml \ | |
| --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| - name: Prepare artifacts | |
| run: | | |
| ( | |
| rm -rf /tmp/artifacts | |
| mkdir -p /tmp/artifacts/packages | |
| cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
| find -name .cache | xargs rm -rf || true | |
| for n in index.html channeldata.json linux-64 osx-64 noarch; do | |
| cp -rv $n /tmp/artifacts/packages || true | |
| done | |
| ) || true | |
| - name: Archive packages | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: osx-packages | |
| path: | | |
| /tmp/artifacts | |
| # Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI. | |
| # build_and_test-osx-arm64: | |
| # name: OSX-ARM64 Tests | |
| # runs-on: macOS-14 # M1 | |
| # strategy: | |
| # fail-fast: true | |
| # max-parallel: 4 | |
| # needs: build-linux | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # # bail if there's no osx-arm64 recipes | |
| # - name: Check for Additional Platforms | |
| # id: additional_platforms | |
| # run: | | |
| # result=$(./scripts/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" "${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" >> $GITHUB_PATH | |
| # - name: Fetch conda install script | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # run: | | |
| # wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| # - name: Set up bioconda-utils | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # run: bash install-and-set-up-conda.sh | |
| # - name: Configure conda | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # run: bash configure-conda.sh | |
| # - name: Build and Test | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # env: | |
| # # Mimic circleci | |
| # OSTYPE: "darwin" | |
| # CI: "true" | |
| # run: | | |
| # set -xe | |
| # eval "$(conda shell.bash hook)" | |
| # conda activate bioconda | |
| # source common.sh | |
| # # Sets up OSX SDK | |
| # run_conda_forge_build_setup | |
| # if [ -z "$GITHUB_BASE_REF" ] ; then | |
| # export GITHUB_BASE_REF="master" | |
| # fi | |
| # git fetch origin "$GITHUB_BASE_REF" | |
| # bioconda-utils build recipes config.yml \ | |
| # --lint --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| # - name: Prepare artifacts | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # run: | | |
| # ( | |
| # rm -rf /tmp/artifacts | |
| # mkdir -p /tmp/artifacts/packages | |
| # cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
| # find -name .cache | xargs rm -rf || true | |
| # for n in index.html channeldata.json osx-arm64 noarch; do | |
| # cp -rv $n /tmp/artifacts/packages || true | |
| # done | |
| # ) || true | |
| # - name: Archive packages | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: osx-arm64-packages | |
| # path: | | |
| # /tmp/artifacts |