✨ Add some handling for user-defined BIDSy atlases #372
Workflow file for this run
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| # Copyright (C) 2022-2023 C-PAC Developers | |
| # This file is part of C-PAC. | |
| # C-PAC is free software: you can redistribute it and/or modify it under | |
| # the terms of the GNU Lesser General Public License as published by the | |
| # Free Software Foundation, either version 3 of the License, or (at your | |
| # option) any later version. | |
| # C-PAC is distributed in the hope that it will be useful, but WITHOUT | |
| # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or | |
| # FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public | |
| # License for more details. | |
| # You should have received a copy of the GNU Lesser General Public | |
| # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>. | |
| name: Build and test C-PAC | |
| on: | |
| push: | |
| jobs: | |
| check-updated-preconfigs: | |
| name: Check if preconfigs need updated | |
| outputs: | |
| phase_one: ${{ steps.rebuild.outputs.phase_one }} | |
| rebuild_phase_one: ${{ steps.rebuild.outputs.rebuild_phase_one }} | |
| phase_two: ${{ steps.rebuild.outputs.phase_two }} | |
| rebuild_phase_two: ${{ steps.rebuild.outputs.rebuild_phase_two }} | |
| phase_three: ${{ steps.rebuild.outputs.phase_three }} | |
| rebuild_phase_three: ${{ steps.rebuild.outputs.rebuild_phase_three }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out C-PAC | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.9' | |
| cache: 'pip' | |
| - name: Check if version updated | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "Theodore (Machine User)" | |
| GITHUB_BRANCH=$(echo ${GITHUB_REF} | cut -d '/' -f 3-) | |
| export PYTHONPATH=$PWD | |
| pip install -q wheel | |
| pip install -q nipype numpy matplotlib pandas pathvalidate pytz pyyaml voluptuous | |
| python ./CPAC/utils/configuration/yaml_template.py | |
| if [[ ! -z $(git diff origin/${GITHUB_BRANCH}) ]] | |
| then | |
| git add CPAC/resources/configs | |
| git commit -m ":bulb: Update comments based on default preconfig" | |
| fi | |
| COMMIT_MESSAGE=$(git log -1 --pretty=%B) | |
| if [[ ! "$COMMIT_MESSAGE" == *"Update version to"* ]] | |
| then | |
| cd CPAC | |
| VERSION=$(python -c "from info import __version__; print(('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__).split('+', 1)[0])") | |
| cd .. | |
| echo "v${VERSION}" > version | |
| find ./CPAC/resources/configs -name "*.yml" -exec sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" {} \; | |
| git add version | |
| VERSIONS=($(git diff origin/${GITHUB_BRANCH} -- version | tail -n 2)) | |
| export PATTERN="(declare|typeset) -a" | |
| if [[ "$(declare -p VERSIONS)" =~ $PATTERN ]] | |
| then | |
| for DOCKERFILE in $(find ./.github/Dockerfiles -name "*.Dockerfile") | |
| do | |
| export IFS="" | |
| for LINE in $(grep "FROM ghcr\.io/fcp\-indi/c\-pac/.*\-${VERSIONS[0]:1}" ${DOCKERFILE}) | |
| do | |
| echo "Updating stage tags in ${DOCKERFILE}" | |
| sed -i "s/\-${VERSIONS[0]:1}/\-${VERSIONS[1]:1}/g" ${DOCKERFILE} | |
| done | |
| done | |
| unset IFS | |
| fi | |
| if [[ ! -z $(git diff origin/${GITHUB_BRANCH}) ]] | |
| then | |
| git add CPAC/resources/configs .github/Dockerfiles | |
| git commit -m ":bookmark: Update version to ${VERSION} ($COMMIT_MESSAGE)" || true | |
| git push origin HEAD:${GITHUB_BRANCH} || true | |
| fi | |
| cd .. | |
| fi | |
| if [[ "${GITHUB_REF_TYPE}" == "tag" ]] | |
| then | |
| cd $HOME/work/C-PAC/C-PAC | |
| for DOCKERFILE in $(ls .github/Dockerfiles/C-PAC.develop-*.Dockerfile) | |
| do | |
| if [[ "$DOCKERFILE" =~ .*C-PAC.develop-(.*)-(bionic|xenial).Dockerfile ]] | |
| then | |
| cp $DOCKERFILE variant-${BASH_REMATCH[1]}.Dockerfile | |
| else | |
| cp $DOCKERFILE Dockerfile | |
| fi | |
| done | |
| git add *ockerfile | |
| git commit -m ":truck: Copy develop Dockerfiles to root directory \ | |
| \ | |
| [skip ci]" | |
| git push origin HEAD:${GITHUB_BRANCH} || true | |
| fi | |
| - name: Get changed files since last commit | |
| uses: tj-actions/[email protected] | |
| id: changed-files | |
| with: | |
| since_last_remote_commit: "true" | |
| files: .github/Dockerfiles/* | |
| json: "true" | |
| - name: Determine stages to rebuild | |
| env: | |
| MESSAGE: ${{ github.event.head_commit.message }} | |
| id: rebuild | |
| run: | | |
| # initialize phase arrays | |
| declare -a PHASE_ONE PHASE_TWO PHASE_THREE REBUILD_PHASE_ONE REBUILD_PHASE_TWO REBUILD_PHASE_THREE | |
| # turn JSON array into BASH array | |
| CHANGED_FILES=( $(echo ${{ steps.changed-files.outputs.all_changed_files }} | sed -e 's/\[//g' -e 's/\]//g' -e 's/\,/ /g') ) | |
| # loop through stages to maybe rebuild | |
| for STAGE in $(cat ${GITHUB_WORKSPACE}/.github/stage_requirements/phase_one.txt) | |
| do | |
| PHASE_ONE+=($STAGE) | |
| # check commit message for [rebuild STAGE] or if STAGE has changed | |
| if [[ "${MESSAGE}" == *"[rebuild ${STAGE}]"* ]] || [[ " ${CHANGED_FILES[*]} " =~ " ${STAGE} " ]] | |
| then | |
| REBUILD_PHASE_ONE+=($STAGE) | |
| fi | |
| done | |
| for STAGE in $(cat ${GITHUB_WORKSPACE}/.github/stage_requirements/phase_two.txt) | |
| do | |
| PHASE_TWO+=($STAGE) | |
| if [[ "${MESSAGE}" == *"[rebuild ${STAGE}]"* ]] || [[ " ${CHANGED_FILES[*]} " =~ " ${STAGE} " ]] | |
| then | |
| REBUILD_PHASE_TWO+=($STAGE) | |
| fi | |
| done | |
| for STAGE in $(cat ${GITHUB_WORKSPACE}/.github/stage_requirements/phase_three.txt) | |
| do | |
| PHASE_THREE+=($STAGE) | |
| if [[ "${MESSAGE}" == *"[rebuild ${STAGE}]"* ]] || [[ "${MESSAGE}" == *"[rebuild base-${STAGE}]"* ]] || [[ " ${CHANGED_FILES[*]} " =~ " ${STAGE} " ]] | |
| then | |
| REBUILD_PHASE_THREE+=($STAGE) | |
| fi | |
| done | |
| # add base stages based on their dependencies | |
| BASES=("${PHASE_THREE[@]}" standard) | |
| if [[ "${MESSAGE}" == *"[rebuild standard]"* ]] || [[ "${MESSAGE}" == *"[rebuild base-standard]"* ]] || [[ " ${CHANGED_FILES[*]} " =~ " standard " ]] | |
| then | |
| REBUILD_PHASE_THREE+=(standard) | |
| fi | |
| for BASE in $BASES | |
| do | |
| for STAGE in $(cat ${GITHUB_WORKSPACE}/.github/stage_requirements/${BASE}.txt) | |
| do | |
| if ([[ " ${REBUILD_PHASE_ONE[*]} " =~ " ${STAGE} " ]] || [[ " ${REBUILD_PHASE_TWO[*]} " =~ " ${STAGE} " ]]) && [[ ! " ${REBUILD_PHASE_THREE[*]} " =~ " ${STAGE} " ]] | |
| then | |
| REBUILD_PHASE_THREE+=($BASE) | |
| fi | |
| done | |
| done | |
| # send stages to rebuild as JSON strings to job outputs | |
| phase_one=$(jq --compact-output --null-input '$ARGS.positional' --args -- ${PHASE_ONE[@]}) | |
| rebuild_phase_one=$(jq --compact-output --null-input '$ARGS.positional' --args -- ${REBUILD_PHASE_ONE[@]}) | |
| phase_two=$(jq --compact-output --null-input '$ARGS.positional' --args -- ${PHASE_TWO[@]}) | |
| rebuild_phase_two=$(jq --compact-output --null-input '$ARGS.positional' --args -- ${REBUILD_PHASE_TWO[@]}) | |
| phase_three=$(jq --compact-output --null-input '$ARGS.positional' --args -- ${PHASE_THREE[@]}) | |
| rebuild_phase_three=$(jq --compact-output --null-input '$ARGS.positional' --args -- ${REBUILD_PHASE_THREE[@]}) | |
| echo "phase_one=${phase_one}" >> $GITHUB_OUTPUT | |
| echo "rebuild_phase_one=${rebuild_phase_one}" >> $GITHUB_OUTPUT | |
| echo "phase_two=${phase_two}" >> $GITHUB_OUTPUT | |
| echo "rebuild_phase_two=${rebuild_phase_two}" >> $GITHUB_OUTPUT | |
| echo "phase_three=${phase_three}" >> $GITHUB_OUTPUT | |
| echo "rebuild_phase_three=${rebuild_phase_three}" >> $GITHUB_OUTPUT | |
| build-stages: | |
| name: Build multistage image stages | |
| needs: check-updated-preconfigs | |
| uses: ./.github/workflows/build_and_test.yml | |
| secrets: inherit | |
| with: | |
| phase_one: ${{ needs.check-updated-preconfigs.outputs.phase_one }} | |
| rebuild_phase_one: ${{ needs.check-updated-preconfigs.outputs.rebuild_phase_one }} | |
| phase_two: ${{ needs.check-updated-preconfigs.outputs.phase_two }} | |
| rebuild_phase_two: ${{ needs.check-updated-preconfigs.outputs.rebuild_phase_two }} | |
| phase_three: ${{ needs.check-updated-preconfigs.outputs.phase_three }} | |
| rebuild_phase_three: ${{ needs.check-updated-preconfigs.outputs.rebuild_phase_three }} |