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.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| #!/bin/bash | ||
|
|
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| # Copyright (C) 2024 C-PAC Developers | ||
|
|
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| # 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/>. | ||
|
|
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| # Update version comment strings | ||
| 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 | ||
| export _SED_COMMAND="s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" | ||
| if [[ "$OSTYPE" == "darwin"* ]]; then | ||
| # Mac OSX | ||
| find ./CPAC/resources/configs -name "*.yml" -exec sed -i '' -E "${_SED_COMMAND}" {} \; | ||
| else | ||
| # Linux and others | ||
| find ./CPAC/resources/configs -name "*.yml" -exec sed -i'' -r "${_SED_COMMAND}" {} \; | ||
| fi | ||
| git add version | ||
| VERSIONS=( `git show $(git log --pretty=format:'%h' -n 2 version | tail -n 1):version` `cat version` ) | ||
| export PATTERN="(declare|typeset) -a" | ||
| if [[ "$(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]}" ${DOCKERFILE}) | ||
| do | ||
| echo "Updating stage tags in ${DOCKERFILE}" | ||
| if [[ "$OSTYPE" == "darwin"* ]]; then | ||
| # Mac OSX | ||
| sed -i "" "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE} | ||
| else | ||
| # Linux and others | ||
| sed -i "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE} | ||
| fi | ||
| done | ||
| done | ||
| unset IFS | ||
| fi | ||
| git add CPAC/resources/configs .github/Dockerfiles | ||
|
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| # Overwrite top-level Dockerfiles with the CI Dockerfiles | ||
| cp .github/Dockerfiles/C-PAC.develop-jammy.Dockerfile Dockerfile | ||
| cp .github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile variant-ABCD-HCP.Dockerfile | ||
| cp .github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile variant-fMRIPrep-LTS.Dockerfile | ||
| cp .github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile variant-lite.Dockerfile | ||
| git add *Dockerfile |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -35,77 +35,8 @@ jobs: | |
| uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 2 | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: '3.9' | ||
| cache: 'pip' | ||
| - name: Check if version updated | ||
| id: version_updated | ||
| run: | | ||
| git config --global user.email "[email protected]" | ||
| git config --global user.name "Theodore (Machine User)" | ||
| GITHUB_BRANCH=$(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/changed-files@v35.7.6 | ||
| uses: tj-actions/changed-files@v41.0.0 | ||
| id: changed-files | ||
| with: | ||
| since_last_remote_commit: "true" | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| # Copyright (C) 2024 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/>. | ||
|
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||
| repos: | ||
| - repo: local | ||
| hooks: | ||
| - id: autoversioning | ||
| name: Update Dockerfiles and version comments | ||
| entry: .github/scripts/autoversioning.sh | ||
| language: script | ||
| files: '.*Dockerfile$|.*\.yaml$|^CPAC/info\.py$' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,37 +1,42 @@ | ||
| # Copyright (C) 2022-2024 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/>. | ||
| """ | ||
| Configurable Pipeline for the Analysis of Connectomes | ||
| ===================================================== | ||
| CPAC is a configurable, open-source, Nipype-based, automated processing | ||
| pipeline for resting state functional MRI (R-fMRI) data, for use by | ||
| both novice and expert users. | ||
| """ | ||
|
|
||
| Copyright (C) 2022 C-PAC Developers | ||
| This file is part of C-PAC. | ||
| from .info import __version__ | ||
| version = __version__ | ||
|
|
||
| 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. | ||
| def _docs_prefix() -> str: | ||
| """Get the docs URL prefix for this version""" | ||
| from CPAC.utils.docs import DOCS_URL_PREFIX | ||
| return DOCS_URL_PREFIX | ||
|
|
||
| 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/>. | ||
| """ | ||
|
|
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| from .info import __version__ | ||
| version = __version__ | ||
| _url_version = 'nightly' if __version__.endswith( | ||
| '-dev') or __version__.endswith('.dev') else f'v{__version__.lstrip("v")}' | ||
| docs_prefix = f'https://fcp-indi.github.io/docs/{_url_version}' | ||
| license_notice = f"""Copyright (C) 2022 C-PAC Developers. | ||
| license_notice = f"""Copyright (C) 2022-2024 C-PAC Developers. | ||
| This program comes with ABSOLUTELY NO WARRANTY. This is free software, | ||
| and you are welcome to redistribute it under certain conditions. For | ||
| details, see {docs_prefix}/license or the COPYING and | ||
| details, see {_docs_prefix()}/license or the COPYING and | ||
| COPYING.LESSER files included in the source code.""" | ||
| __all__ = ['license_notice', 'version', '__version__'] |
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