Deleted the loose motion file from cpac_outputs.tsv #795
Workflow file for this run
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| name: Check updated preconfigs | |
| on: | |
| push: | |
| jobs: | |
| check-updated-preconfigs: | |
| name: Check if preconfigs need updated | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out C-PAC | |
| uses: actions/checkout@v2 | |
| 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 yamlordereddictloader | |
| 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 | |
| trigger-next-workflow: | |
| needs: check-updated-preconfigs | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up check | |
| uses: Sibz/[email protected] | |
| with: | |
| authToken: ${{ secrets.ACTIONS_WORKFLOW_TOKEN }} | |
| context: "Build C-PAC images" | |
| state: pending | |
| - name: Check out C-PAC | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 2 | |
| - name: Build stages | |
| if: github.ref_type == 'branch' | |
| run: | | |
| pip install PyGithub | |
| BASE_REFS=$(python .github/scripts/get_pr_base_shas.py) | |
| if [ -n "$BASE_REFS" ] | |
| then | |
| for REF in $BASE_REFS | |
| do | |
| echo "Running against base $REF" | |
| gh workflow run build_stages.yml --ref ${GITHUB_REF_NAME} -f base_ref="$REF" | |
| done | |
| else | |
| echo "Running against last PR" | |
| gh workflow run build_stages.yml --ref ${GITHUB_REF_NAME} | |
| fi | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.ACTIONS_WORKFLOW_TOKEN }} | |
| - name: Build, test, and push C-PAC | |
| if: github.ref_type == 'tag' | |
| run: | | |
| pip install PyGithub | |
| gh workflow run build_and_test.yml --ref ${GITHUB_REF_NAME} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.ACTIONS_WORKFLOW_TOKEN }} |