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| Original file line number | Diff line number | Diff line change |
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| #!/bin/bash | ||
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| # Check to see if any changed recipes have specified the key | ||
| # extra:additional-platforms, and if so, if they match the platform of the | ||
| # currently-running machine. | ||
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| # arguments | ||
| git_range=$1 | ||
| job_name=$2 | ||
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| # Download ARM version of yq | ||
| yq_platform=$(uname) | ||
| yq_arch=$(uname -m) | ||
| [[ $yq_arch = "aarch64" ]] && yq_arch="arm64" | ||
| mkdir -p ${HOME}/bin | ||
| wget https://github.com/mikefarah/yq/releases/latest/download/yq_${yq_platform}_${yq_arch} -O ${HOME}/bin/yq | ||
| chmod +x ${HOME}/bin/yq | ||
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| # Find recipes changed from this merge | ||
| files=`git diff --name-only --diff-filter AMR ${git_range} | grep -E 'meta.yaml$' ` | ||
| build=0 | ||
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| for file in $files; do | ||
| echo $file | ||
| # To create a properly-formatted yaml that yq can parse, comment out jinja2 | ||
| # variable setting with {% %} and remove variable use with {{ }}. | ||
| additional_platforms=$(cat $file \ | ||
| | sed -E 's/(.*)\{%(.*)%\}(.*)/# \1\2\3/g' \ | ||
| | tr -d '{{' | tr -d '}}' \ | ||
| | ${HOME}/bin/yq '.extra.additional-platforms[]') | ||
| # Check if any additional platforms match this job | ||
| for additional_platform in $additional_platforms; do | ||
| if [ "${CIRCLE_JOB}" = "${job_name}-${additional_platform}" ] | ||
| then | ||
| build=1 | ||
| break | ||
| fi | ||
| done | ||
| done | ||
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| # If no changed recipes apply to this platform, skip remaining steps | ||
| if [[ build -lt 1 ]] | ||
| then | ||
| echo "No recipes using this platform, skipping rest of job." | ||
| circleci-agent step halt | ||
| fi |
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| # .circleci/config.yml | ||
| version: 2.1 | ||
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| executors: | ||
| # osx-arm64: | ||
| # macos: | ||
| # xcode: 14.2.0 # indicate your selected version of Xcode | ||
| # resource_class: macos.m1.large.gen1 | ||
| linux-aarch64: | ||
| machine: | ||
| image: ubuntu-2204:current | ||
| resource_class: arm.medium | ||
|
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| jobs: # a basic unit of work in a run | ||
| build_and_test: | ||
| parameters: | ||
| os: | ||
| type: executor | ||
| executor: << parameters.os >> | ||
| steps: | ||
| - checkout | ||
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|
||
| - run: | ||
| name: Check for Additional Platforms | ||
| command: ./.circleci/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" | ||
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| - run: | ||
| name: Fetch bioconda install script | ||
| command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh | ||
|
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||
| - run: | ||
| name: Install bioconda-utils | ||
| command: | | ||
| sudo mkdir -p /opt/ | ||
| sudo chmod o+rwx /opt | ||
| bash install-and-set-up-conda.sh | ||
| - run: | ||
| name: Setup PATH | ||
| command: | ||
| echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" | ||
|
|
||
| # We 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 by --system). | ||
| - run: | ||
| name: Configure conda | ||
| command: bash configure-conda.sh | ||
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||
| - run: | ||
| name: Build and test | ||
| command: | | ||
| . common.sh | ||
| source /opt/mambaforge/etc/profile.d/conda.sh | ||
| source /opt/mambaforge/etc/profile.d/mamba.sh | ||
| mamba activate bioconda | ||
| bioconda-utils build recipes config.yml \ | ||
| --lint --docker --mulled-test \ | ||
| --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \ | ||
| --git-range origin/master HEAD | ||
| - run: | ||
| name: Prepare artifacts | ||
| command: | | ||
| ( | ||
| 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-aarch64 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 ${1} ." | ||
| ' -- | ||
| fi | ||
| ) || true | ||
| - store_artifacts: | ||
| path: /tmp/artifacts | ||
|
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||
| build_and_upload: | ||
| parameters: | ||
| os: | ||
| type: executor | ||
| executor: << parameters.os >> | ||
| steps: | ||
| - checkout | ||
|
|
||
| - run: | ||
| name: Check for Additional Platforms | ||
| command: ./.circleci/check-for-additional-platforms.sh "${CIRCLE_SHA1}~1 ${CIRCLE_SHA1}" "build_and_upload" | ||
|
|
||
| - run: | ||
| name: Fetch bioconda install script | ||
| command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh | ||
|
|
||
| - run: | ||
| name: Install bioconda-utils | ||
| command: | | ||
| sudo mkdir -p /opt | ||
| sudo chmod o+rwx /opt | ||
| bash install-and-set-up-conda.sh | ||
| - run: | ||
| name: Setup PATH | ||
| command: | ||
| echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" | ||
|
|
||
| # We 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 by --system). | ||
| - run: | ||
| name: Configure conda | ||
| command: bash configure-conda.sh | ||
|
|
||
| - run: | ||
| name: Build and push | ||
| command: | | ||
| source /opt/mambaforge/etc/profile.d/conda.sh | ||
| source /opt/mambaforge/etc/profile.d/mamba.sh | ||
| mamba activate bioconda | ||
| bioconda-utils handle-merged-pr recipes config.yml \ | ||
| --repo bioconda/bioconda-recipes \ | ||
| --git-range ${CIRCLE_SHA1}~1 ${CIRCLE_SHA1} \ | ||
| --fallback build \ | ||
| --artifact-source circleci | ||
| bulk_build: | ||
| parameters: | ||
| os: | ||
| type: executor | ||
| runner: | ||
| type: integer | ||
| executor: << parameters.os >> | ||
| steps: | ||
| - add_ssh_keys: | ||
| fingerprints: | ||
| - 1e:85:74:42:35:5f:c5:a2:35:c2:ec:b7:80:c0:7c:40 | ||
|
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||
| - checkout | ||
|
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||
| - run: | ||
| name: Check for [ci run] | ||
| command: | | ||
| commit_message="$(git log --format=oneline -n 1 $CIRCLE_SHA1)" | ||
| if [[ $commit_message =~ "[ci run]" ]]; then | ||
| echo "[ci run] found, continuing." | ||
| else | ||
| echo "[ci run] not found, exiting." | ||
| circleci-agent step halt | ||
| fi | ||
| - run: | ||
| name: set git user | ||
| command: | | ||
| git config user.name BiocondaBot | ||
| git config user.email [email protected] | ||
| git branch --set-upstream-to=origin/$CIRCLE_BRANCH $CIRCLE_BRANCH | ||
| - run: | ||
| name: Fetch bioconda install script | ||
| command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh | ||
|
|
||
| - run: | ||
| name: Install bioconda-utils | ||
| command: | | ||
| sudo mkdir -p /opt/ | ||
| sudo chmod o+rwx /opt | ||
| bash install-and-set-up-conda.sh | ||
| - run: | ||
| name: Setup PATH | ||
| command: | ||
| echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" | ||
|
|
||
| # We reconfigure conda to use the right channel setup. | ||
| # This has to be done after the cache is restored, because | ||
| # the channel setup is not cached as it resides in the home directory. | ||
| # We could use a system-wide (and therefore cached) channel setup, | ||
| # but mamba does not support that at the time of implementation | ||
| # (it ignores settings made by --system). | ||
| - run: | ||
| name: Configure conda | ||
| command: bash configure-conda.sh | ||
|
|
||
| # For now, do not upload ARM images to biocontainers: --mulled-upload-target biocontainers | ||
| - run: | ||
| name: Build and upload | ||
| command: | | ||
| set -e | ||
| . common.sh | ||
| source /opt/mambaforge/etc/profile.d/conda.sh | ||
| source /opt/mambaforge/etc/profile.d/mamba.sh | ||
| mamba activate bioconda | ||
| echo '============' | ||
| conda info --all | ||
| conda config --show-sources | ||
| python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' | ||
| echo '============' | ||
| bioconda-utils build recipes config.yml \ | ||
| --worker-offset << parameters.runner >> --n-workers 6 \ | ||
| --docker --mulled-test --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \ | ||
| --anaconda-upload \ | ||
| --mulled-upload-target biocontainers \ | ||
| --record-build-failures \ | ||
| --skiplist-leafs | ||
| conda clean -y --all | ||
| workflows: | ||
| build and test (ARM): | ||
| jobs: | ||
| - build_and_test: | ||
| filters: | ||
| branches: | ||
| ignore: | ||
| - master | ||
| - bulk | ||
| matrix: | ||
| parameters: | ||
| os: | ||
| #- osx-arm64 | ||
| - linux-aarch64 | ||
|
|
||
| build and upload (ARM): | ||
| jobs: | ||
| - build_and_upload: | ||
| filters: | ||
| branches: | ||
| only: master | ||
| matrix: | ||
| parameters: | ||
| os: | ||
| #- osx-arm64 | ||
| - linux-aarch64 | ||
|
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||
| Bulk branch (ARM): | ||
| jobs: | ||
| - bulk_build: | ||
| filters: | ||
| branches: | ||
| only: bulk | ||
| matrix: | ||
| parameters: | ||
| os: | ||
| #- osx-arm64 | ||
| - linux-aarch64 | ||
| runner: [0, 1, 2, 3, 4, 5] |
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