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| Original file line number | Diff line number | Diff line change |
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| @@ -1,149 +1,27 @@ | ||
| name: Apptainer Build | ||
| on: workflow_dispatch | ||
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| jobs: | ||
| build-and-push-image: | ||
| runs-on: ubuntu-latest | ||
| name: Build Apptainer image | ||
| permissions: | ||
| contents: read | ||
| packages: write | ||
| contents: read | ||
| packages: write | ||
| steps: | ||
| - name: Install Apptainer | ||
| uses: uw-psych/apptainer-actions/setup@main | ||
| uses: uw-psych/apptainer-actions/setup@dev | ||
| - name: Check out code for the container build | ||
| uses: actions/checkout@v4 | ||
| - name: Get version | ||
| shell: bash | ||
| run: | | ||
| if [[ "${GITHUB_REF_TYPE:-}" == "tag" ]]; then | ||
| case "${GITHUB_REF_NAME:-}" in | ||
| v?*) IMAGE_VERSION="${GITHUB_REF_NAME#v}";; | ||
| *@?*) IMAGE_VERSION="${GITHUB_REF_NAME#*@}";; | ||
| *) echo "Invalid tag: \"${GITHUB_REF_NAME:-}\"" >&2; exit 1;; | ||
| esac | ||
| echo "IMAGE_VERSION=${IMAGE_VERSION}" >> "${GITHUB_ENV}" | ||
| fi | ||
| - name: Build container for workshop-01/single-job.py | ||
| - name: Build Container for Workshop 1 (single-job.py) | ||
| uses: uw-psych/apptainer-actions/build-and-push@dev | ||
| with: | ||
| deffile: workshop-01/Singularity | ||
| build_args: 'PY_FILE=single-job.py' | ||
|
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| - | ||
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| name: Build and Deploy Apptainer Container | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| defaults: | ||
| run: | ||
| shell: bash | ||
|
|
||
| env: | ||
| GH_TOKEN: ${{ github.token }} | ||
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||
| jobs: | ||
| find-changed-images: | ||
| runs-on: ubuntu-latest | ||
| name: Find Changed Apptainer Containers | ||
| outputs: | ||
| image_names: ${{ steps.find-changed-deffiles.outputs.defs_to_build }} | ||
| n_defs_to_build: ${{ steps.find-changed-deffiles.outputs.n_defs_to_build }} | ||
| steps: | ||
| - name: Check out code for the container build | ||
| uses: actions/checkout@v4 | ||
| - name: Find definition files of changed containers | ||
| id: find-changed-deffiles | ||
| run: | | ||
| set -ux | ||
| function find_singularity_files_deps() { | ||
| # Find all files that are dependencies of a Singularity definition file. | ||
| local __deffile="$1" | ||
| local __curdir="${PWD}" | ||
| echo "$(cd "$(dirname "${__deffile}")" && sed -nE '1,/^\s*%files\b/d; /^\s*%.*/q; s/^\s*//g; s/([^\])\s+.*$/\1/g; /^\s*$/d; p' "$(basename ${__deffile})" | paste -sd ' ' | xargs find | xargs realpath --logical --no-symlinks --relative-to="${__curdir}" | sort | uniq)" | ||
| } | ||
| found_deffiles=() | ||
| found_deffiles+="$(find . -type f \( -name 'Singularity' -o -name '*.def' -o -name 'Apptainer' \) || true)" | ||
| built_images="$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" '/users/maouw/packages?package_type=container' --jq '. [] | select(.repository.name == "${{ github.repository }}" | .name' | wc -l | cut -f1 -d' ')" | ||
| changed_files="$(git diff --name-only HEAD HEAD~1 || true)" | ||
| if [[ "${#found_deffiles[@]}" > 0 ]]; then | ||
| for deffile in "${found_deffiles[@]}"; do | ||
| if [[ -n "${deffile:-}" ]] && [[ -r "${deffile}" ]]; then | ||
| echo "Found container definition file \"${deffile}\"" | ||
| if git diff --name-only HEAD HEAD~1 | grep -q -F -f <(echo "${deffile}"; find_singularity_files_deps "${deffile}"); then | ||
| echo "Found changes to files that are dependencies of \"${deffile}\"" | ||
| defs_to_build+=("${deffile}") | ||
| fi | ||
| fi | ||
| done | ||
| fi | ||
| [[ "${#defs_to_build[@]}" > 0 ]] && echo "defs_to_build=\"${defs_to_build[*]}\"" >> "$GITHUB_OUTPUT" && echo "n_defs_to_build=${#defs_to_build[@]}" >> "$GITHUB_OUTPUT" | ||
| build-and-push-images: | ||
| needs: find-changed-images | ||
| runs-on: ubuntu-latest | ||
| name: Build and Deploy Apptainer Containers | ||
| permissions: | ||
| contents: read | ||
| packages: write | ||
| # if: ${{ needs.find-changed-images.outputs.n_defs_to_build }} > 0 | ||
| steps: | ||
| - name: Check out code for the container build | ||
| uses: actions/checkout@v4 | ||
| - name: Delete misc tools to free space | ||
| run: | | ||
| sudo rm -rf \ | ||
| /usr/share/dotnet \ | ||
| /opt/ghc \ | ||
| /usr/local/lib/android \ | ||
| /usr/local/share/powershell \ | ||
| /usr/share/swift || true | ||
| - name: Download and Install Apptainer | ||
| run: | | ||
| set -euxo pipefail | ||
| APPTAINER_LATEST_TAGNAME="$(gh release view --repo apptainer/apptainer --json tagName -t '{{.tagName}}' | head -n 1)" | ||
| [[ -n "${APPTAINER_LATEST_TAGNAME}" ]] || { echo "No latest tag found for apptainer/apptainer"; exit 1; } | ||
| echo "Latest tag for apptainer/apptainer is \"${APPTAINER_LATEST_TAGNAME}\"" | ||
| gh release download --repo apptainer/apptainer --pattern 'apptainer_*_amd64.deb' --skip-existing -O "${SETUP_DOWNLOADS_DIR}/apptainer_${APPTAINER_LATEST_TAGNAME}.deb" "${APPTAINER_LATEST_TAGNAME}" | ||
| sudo dpkg --install --force-depends "${SETUP_DOWNLOADS_DIR}/apptainer_${APPTAINER_LATEST_TAGNAME}.deb" && sudo apt-get install --fix-broken --yes --quiet | ||
| apptainer --version | ||
| - name: Download and Install oras-cli | ||
| run: | | ||
| set -euxo pipefail | ||
| ORAS_LATEST_TAGNAME="$(gh release view --repo oras-project/oras --json tagName -t '{{.tagName}}' | head -n 1)" | ||
| [[ -n "${ORAS_LATEST_TAGNAME}" ]] || { echo "No latest tag found for oras-project/oras"; exit 1; } | ||
| echo "Latest tag for oras-project/oras is \"${ORAS_LATEST_TAGNAME}\"" | ||
| gh release download --repo oras-project/oras --pattern '*linux_amd64.tar.gz' --skip-existing -O "${SETUP_DOWNLOADS_DIR}/oras_${ORAS_LATEST_TAGNAME}.tar.gz" "${ORAS_LATEST_TAGNAME}" | ||
| sudo mkdir -p /opt/local/bin | ||
| sudo tar -xzf "${SETUP_DOWNLOADS_DIR}/oras_${ORAS_LATEST_TAGNAME}.tar.gz" -C /opt/local/bin oras && sudo chmod +x /opt/local/bin/oras | ||
| export PATH="/opt/local/bin:${PATH}" | ||
| echo "PATH=${PATH}" >> $GITHUB_ENV | ||
| oras version | ||
| - name: Build Container | ||
| run: | | ||
| set -euxo pipefail | ||
| echo "Defs to build: \"${{ needs.find-changed-images.outputs.defs_to_build }}\"" | ||
| apptainer remote login -u ${{ github.actor }} -p ${{ secrets.TOKEN }} oras://ghcr.io | ||
| for deffile in ${{ needs.find-changed-images.outputs.image_names}}; do | ||
| { [[ -n "${deffile:-}" ]] && [[ -r "${deffile}" ]] ; } || break | ||
| DEF_DIR="$(dirname "${deffile}")" | ||
| pushd "${DEF_DIR}" | ||
| IMAGE_NAME="$(basename "${PWD}")" | ||
| IMAGE_TAG="$(git rev-parse --short HEAD)" | ||
| echo "Building \"${IMAGE_NAME}.sif\"" | ||
| apptainer build --fix-perms --force "${IMAGE_NAME}.sif" "${IMAGE_NAME}" || { echo "Failed to build \"${IMAGE_NAME}.sif\""; exit 1; } | ||
| echo "Built \"${IMAGE_NAME}.sif\"" | ||
| echo "Pushing \"sif/${IMAGE_NAME}.sif\" to ghcr.io/${{ github.repository }}/${IMAGE_NAME}:${IMAGE_TAG}" | ||
| apptainer push -U "sif/${IMAGE_NAME}.sif" oras://ghcr.io/${{ github.repository }}/${IMAGE_NAME}:${IMAGE_TAG} || { echo "Failed to push \"sif/${IMAGE_NAME}.sif\' to ghcr.io/${{ github.repository }}/${IMAGE_NAME}:${IMAGE_TAG}"; exit 1; } | ||
| echo "Pushed \"sif/${IMAGE_NAME}.sif\" to ghcr.io/${{ github.repository }}/${IMAGE_NAME}:${IMAGE_TAG}" | ||
| # Add "latest" tag if IMAGE_TAG is not latest | ||
| if [[ "${IMAGE_TAG}" != "latest" ]]; then | ||
| oras login -u ${{ github.actor }} -p ${{ secrets.TOKEN }} ghcr.io | ||
| oras tag ghcr.io/${{ github.repository }}/${IMAGE_NAME}:${IMAGE_TAG} latest | ||
| fi | ||
| rm -f "${IMAGE_NAME}.sif" | ||
| popd | ||
| done | ||
| build-args: PY_FILE=workshop-01/single-job.py | ||
| image-name: w01-single-job | ||
| - name: Build Container for Workshop 1 (array-job.py) | ||
| uses: uw-psych/apptainer-actions/build-and-push@dev | ||
| with: | ||
| deffile: workshop-01/Singularity | ||
| build-args: PY_FILE=workshop-01/array-job.py | ||
| image-name: w01-array-job |