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Merge pull request #2100 from FCP-INDI/rc/v1.8.7
Release v1.8.7
2 parents 6448fed + e098f66 commit 96db8b0

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‎.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile

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FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.6.dev1
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FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.dev1
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LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/e480a8f99534f1b05f37bf44c64827384b69b383/Dockerfile)"
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LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
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USER root

‎.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile

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FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.6.dev1
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FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.dev1
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LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [fMRIPrep LTS](https://reproducibility.stanford.edu/fmriprep-lts#long-term-support-lts)"
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LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
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USER root

‎.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile

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# You should have received a copy of the GNU Lesser General Public
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# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
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FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.6.dev1
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FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.dev1
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LABEL org.opencontainers.image.description "Full C-PAC image"
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LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
2020
USER root

‎.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile

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# You should have received a copy of the GNU Lesser General Public
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# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
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FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.6.dev1
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FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.dev1
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LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer"
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LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
2020
USER root

‎.github/Dockerfiles/base-ABCD-HCP.Dockerfile

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FROM ghcr.io/fcp-indi/c-pac/afni:21.1.00-bionic as AFNI
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FROM ghcr.io/fcp-indi/c-pac/ants:2.2.0.neurodocker-bionic as ANTs
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FROM ghcr.io/fcp-indi/c-pac/c3d:1.0.0-bionic as c3d
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FROM ghcr.io/fcp-indi/c-pac/connectome-workbench:1.3.2-1.neurodebian-bionic as connectome-workbench
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FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-bionic as FreeSurfer
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FROM ghcr.io/fcp-indi/c-pac/fsl:5.0.10-bionic as FSL
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FROM ghcr.io/fcp-indi/c-pac/ica-aroma:0.4.3-beta-bionic as ICA-AROMA
@@ -43,7 +42,7 @@ COPY --from=ANTs /ants_template /ants_template
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# install FSL
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COPY --from=FSL /usr/bin/tclsh /usr/bin/tclsh
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COPY --from=FSL /usr/bin/wish /usr/bin/wish
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COPY --from=FSL /usr/share/fsl/ /usr/share/fsl/
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COPY --from=FSL /usr/share/fsl /usr/share/fsl
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COPY --from=FSL /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
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COPY --from=FSL /usr/lib/lib*so* /usr/lib/
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# set up FSL environment
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PATH=$PATH:/opt/msm/Ubuntu
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# install Connectome Workbench
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COPY --from=connectome-workbench /lib64/* /lib64.
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COPY --from=connectome-workbench /lib/x86_64-linux-gnu/* /lib/x86_64-linux-gnu/
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COPY --from=connectome-workbench /usr/* /usr/
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RUN APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1 apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC && \
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APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1 apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138 && \
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APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1 apt-key adv --keyserver keyserver.ubuntu.com --recv-keys DCC9EFBF77E11517 && \
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printf '\ndeb http://httpredir.debian.org/debian/ buster main non-free' >> /etc/apt/sources.list && \
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apt-get update --allow-insecure-repositories && \
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apt-get install connectome-workbench=1.3.2-1 -y && \
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strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
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ENV PATH=/usr:$PATH
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# install ICA-AROMA
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COPY --from=ICA-AROMA /opt/ICA-AROMA /opt/ICA-AROMA

‎.github/Dockerfiles/base-standard.Dockerfile

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# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
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FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-jammy as FreeSurfer
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FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.6.dev1
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FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.dev1
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LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
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Standard software dependencies for C-PAC standard images"
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LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC

‎.github/scripts/autoversioning.sh

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#!/bin/bash
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# Copyright (C) 2024 C-PAC Developers
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# This file is part of C-PAC.
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# C-PAC is free software: you can redistribute it and/or modify it under
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# the terms of the GNU Lesser General Public License as published by the
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# Free Software Foundation, either version 3 of the License, or (at your
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# option) any later version.
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# C-PAC is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
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# License for more details.
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# You should have received a copy of the GNU Lesser General Public
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# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
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# Update version comment strings
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cd CPAC
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VERSION=$(python -c "from info import __version__; print(('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__).split('+', 1)[0])")
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cd ..
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echo "v${VERSION}" > version
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export _SED_COMMAND="s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g"
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if [[ "$OSTYPE" == "darwin"* ]]; then
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# Mac OSX
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find ./CPAC/resources/configs -name "*.yml" -exec sed -i '' -E "${_SED_COMMAND}" {} \;
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else
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# Linux and others
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find ./CPAC/resources/configs -name "*.yml" -exec sed -i'' -r "${_SED_COMMAND}" {} \;
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fi
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git add version
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VERSIONS=( `git show $(git log --pretty=format:'%h' -n 2 version | tail -n 1):version` `cat version` )
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export PATTERN="(declare|typeset) -a"
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if [[ "$(declare -p VERSIONS)" =~ $PATTERN ]]
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then
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for DOCKERFILE in $(find ./.github/Dockerfiles -name "*.Dockerfile")
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do
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export IFS=""
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for LINE in $(grep "FROM ghcr\.io/fcp\-indi/c\-pac/.*\-${VERSIONS[0]}" ${DOCKERFILE})
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do
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echo "Updating stage tags in ${DOCKERFILE}"
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if [[ "$OSTYPE" == "darwin"* ]]; then
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# Mac OSX
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sed -i "" "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE}
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else
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# Linux and others
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sed -i "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE}
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fi
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done
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done
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unset IFS
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fi
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git add CPAC/resources/configs .github/Dockerfiles
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# Overwrite top-level Dockerfiles with the CI Dockerfiles
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cp .github/Dockerfiles/C-PAC.develop-jammy.Dockerfile Dockerfile
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cp .github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile variant-ABCD-HCP.Dockerfile
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cp .github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile variant-fMRIPrep-LTS.Dockerfile
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cp .github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile variant-lite.Dockerfile
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git add *Dockerfile

‎.github/workflows/on_push.yml

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uses: actions/checkout@v3
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with:
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fetch-depth: 2
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- uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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cache: 'pip'
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- name: Check if version updated
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id: version_updated
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run: |
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git config --global user.email "[email protected]"
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git config --global user.name "Theodore (Machine User)"
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GITHUB_BRANCH=$(echo ${GITHUB_REF} | cut -d '/' -f 3-)
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export PYTHONPATH=$PWD
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pip install -q wheel
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pip install -q nipype numpy matplotlib pandas pathvalidate pytz pyyaml voluptuous
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python ./CPAC/utils/configuration/yaml_template.py
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if [[ ! -z $(git diff origin/${GITHUB_BRANCH}) ]]
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then
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git add CPAC/resources/configs
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git commit -m ":bulb: Update comments based on default preconfig"
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fi
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COMMIT_MESSAGE=$(git log -1 --pretty=%B)
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if [[ ! "$COMMIT_MESSAGE" == *"Update version to"* ]]
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then
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cd CPAC
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VERSION=$(python -c "from info import __version__; print(('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__).split('+', 1)[0])")
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cd ..
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echo "v${VERSION}" > version
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find ./CPAC/resources/configs -name "*.yml" -exec sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" {} \;
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git add version
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VERSIONS=($(git diff origin/${GITHUB_BRANCH} -- version | tail -n 2))
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export PATTERN="(declare|typeset) -a"
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if [[ "$(declare -p VERSIONS)" =~ $PATTERN ]]
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then
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for DOCKERFILE in $(find ./.github/Dockerfiles -name "*.Dockerfile")
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do
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export IFS=""
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for LINE in $(grep "FROM ghcr\.io/fcp\-indi/c\-pac/.*\-${VERSIONS[0]:1}" ${DOCKERFILE})
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do
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echo "Updating stage tags in ${DOCKERFILE}"
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sed -i "s/\-${VERSIONS[0]:1}/\-${VERSIONS[1]:1}/g" ${DOCKERFILE}
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done
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done
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unset IFS
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fi
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if [[ ! -z $(git diff origin/${GITHUB_BRANCH}) ]]
82-
then
83-
git add CPAC/resources/configs .github/Dockerfiles
84-
git commit -m ":bookmark: Update version to ${VERSION} ($COMMIT_MESSAGE)" || true
85-
git push origin HEAD:${GITHUB_BRANCH} || true
86-
fi
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cd ..
88-
fi
89-
if [[ "${GITHUB_REF_TYPE}" == "tag" ]]
90-
then
91-
cd $HOME/work/C-PAC/C-PAC
92-
for DOCKERFILE in $(ls .github/Dockerfiles/C-PAC.develop-*.Dockerfile)
93-
do
94-
if [[ "$DOCKERFILE" =~ .*C-PAC.develop-(.*)-(bionic|xenial).Dockerfile ]]
95-
then
96-
cp $DOCKERFILE variant-${BASH_REMATCH[1]}.Dockerfile
97-
else
98-
cp $DOCKERFILE Dockerfile
99-
fi
100-
done
101-
git add *ockerfile
102-
git commit -m ":truck: Copy develop Dockerfiles to root directory \
103-
\
104-
[skip ci]"
105-
git push origin HEAD:${GITHUB_BRANCH} || true
106-
fi
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- name: Get changed files since last commit
108-
uses: tj-actions/changed-files@v35.7.6
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uses: tj-actions/changed-files@v41.0.0
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id: changed-files
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with:
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since_last_remote_commit: "true"

‎.markdownlint.yml

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# no duplicate headers
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MD024:
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siblings_only: true
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# allow specific inline HTML elements
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MD033:
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allowed_elements:
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- span

‎.pre-commit-config.yaml

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# Copyright (C) 2024 C-PAC Developers
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# This file is part of C-PAC.
4+
5+
# C-PAC is free software: you can redistribute it and/or modify it under
6+
# the terms of the GNU Lesser General Public License as published by the
7+
# Free Software Foundation, either version 3 of the License, or (at your
8+
# option) any later version.
9+
10+
# C-PAC is distributed in the hope that it will be useful, but WITHOUT
11+
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
12+
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
13+
# License for more details.
14+
15+
# You should have received a copy of the GNU Lesser General Public
16+
# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
17+
18+
repos:
19+
- repo: local
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hooks:
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- id: autoversioning
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name: Update Dockerfiles and version comments
23+
entry: .github/scripts/autoversioning.sh
24+
language: script
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files: '.*Dockerfile$|.*\.yaml$|^CPAC/info\.py$'
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- id: update-yaml-comments
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name: Update YAML comments
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entry: CPAC/utils/configuration/yaml_template.py
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language: python
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files: '^CPAC/resources/configs/pipeline_config_.*\.ya?ml'
31+
additional_dependencies:
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- "click"
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- "nipype"
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- "pathvalidate"
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- "pyyaml"
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- "voluptuous"

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