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🧑‍💻 Scripts to deprecate already-published Docker images (#6)
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‎.gitignore‎

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#!/usr/bin/env bash
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# Copyright (C) 2022 C-PAC Developers
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#
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# This file is part of CPAC-Development.
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#
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# CPAC-Development 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.
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#
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# CPAC-Development 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.
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#
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# You should have received a copy of the GNU Lesser General Public License along with CPAC-Development. If not, see <https://www.gnu.org/licenses/>.
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# Files that should be updated fresh each time
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deprecate/cpac_pipeline.py
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deprecate/run.py

‎README.md‎

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<!-- Copyright (C) 2022 C-PAC Developers
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This file is part of CPAC-Development.
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CPAC-Development 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.
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CPAC-Development 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.
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You should have received a copy of the GNU Lesser General Public License along with CPAC-Development. If not, see <https://www.gnu.org/licenses/>. -->
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CPAC-Development
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================

‎deprecate/CRITICAL_ALERT.rst‎

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.. Copyright (C) 2022 C-PAC Developers
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..
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.. This file is part of CPAC-Development.
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..
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.. CPAC-Development 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.
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..
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.. CPAC-Development 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.
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..
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.. You should have received a copy of the GNU Lesser General Public License along with CPAC-Development. If not, see <https://www.gnu.org/licenses/>.
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This version of C-PAC (``${DEPRECATED_VERSION}``) is deprecated due to a bug in ``single_step_resampling``. Unless you have a specific reason to use this version of C-PAC (``${DEPRECATED_VERSION}``), we recommend upgrading to at least version ${RECOMMENDED_MINIMUM_VERSION}. See https://fcp-indi.github.io/docs/latest/user/release_notes/v${RECOMMENDED_MINIMUM_VERSION} for more information about C-PAC v${RECOMMENDED_MINIMUM_VERSION}. To use ${DEPRECATED_VERSION} anyway, you can pull ``fcpindi/c-pac:${DEPRECATED_VERSION}-DEPRECATED`` from Docker Hub.
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Critical Alert for fMRIPrep-Options in C-PAC v1.8.1 - v1.8.3
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============================================================
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* Fixed a bug that was causing ``single_step_resampling``, when combined with certain other configurations, to inadvertently cause unexpected forks in the pipeline past transform application.
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* This bug caused any affected ``fmriprep-options-based`` pipeline configurations (including ``fx-options`` and ``rbc-options``) to produce BOLD time series write-outs to the output directory in template space which were not nuisance regressed or filtered, for C-PAC versions 1.8.1 through 1.8.3.
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* Although these outputs were not expressly labeled as nuisance regressed or filtered, they were labeled as preprocessed with ``desc-preproc`` and were the only functional data transformed to template space and used for downstream processing, such as ROI-based timeseries extraction.
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* If you are unsure if you have been affected, you can check the side-car JSON for your template-space BOLD data from these versions for those pipeline configurations, as the JSON will still accurately reflect what operations had been performed on the data.
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‎deprecate/DEPRECATED.Dockerfile‎

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# Copyright (C) 2022 C-PAC Developers
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# This file is part of CPAC-Development.
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# CPAC-Development 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.
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# CPAC-Development 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.
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# You should have received a copy of the GNU Lesser General Public License along with CPAC-Development. If not, see <https://www.gnu.org/licenses/>.
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ARG DEPRECATED_VERSION
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ARG RECOMMENDED_MINIMUM_VERSION
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FROM bash
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ARG DEPRECATED_VERSION
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ARG RECOMMENDED_MINIMUM_VERSION
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COPY ./CRITICAL_ALERT.rst /CRITICAL_ALERT.rst
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COPY ./entrypoint /entrypoint
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RUN sed -i "s|\${DEPRECATED_VERSION}|${DEPRECATED_VERSION}|g" /CRITICAL_ALERT.rst && \
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sed -i "s|\${RECOMMENDED_MINIMUM_VERSION}|${RECOMMENDED_MINIMUM_VERSION}|g" /CRITICAL_ALERT.rst && \
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ln -s /entrypoint /bin/bash
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ENTRYPOINT [ "/entrypoint" ]

‎deprecate/Dockerfile‎

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# Copyright (C) 2022 C-PAC Developers
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#
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# This file is part of CPAC-Development.
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#
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# CPAC-Development 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.
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#
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# CPAC-Development 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.
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#
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# You should have received a copy of the GNU Lesser General Public License along with CPAC-Development. If not, see <https://www.gnu.org/licenses/>.
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ARG DEPRECATED_VERSION
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FROM fcpindi/c-pac:${DEPRECATED_VERSION}
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ARG DEPRECATED_VERSION
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COPY ./CRITICAL_ALERT.rst /CRITICAL_ALERT.rst
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COPY ./bash.bashrc /etc/bash.bashrc
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RUN sed -i "s|\${DEPRECATED_VERSION}|${DEPRECATED_VERSION}|g" /CRITICAL_ALERT.rst && \
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sed -i "s|\${RECOMMENDED_MINIMUM_VERSION}|${RECOMMENDED_MINIMUM_VERSION}|g" /CRITICAL_ALERT.rst
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COPY ./cpac_pipeline.py /code/CPAC/pipeline/cpac_pipeline.py
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COPY ./run.py /code/run.py

‎deprecate/README.md‎

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<!-- Copyright (C) 2022 C-PAC Developers
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This file is part of CPAC-Development.
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CPAC-Development 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.
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CPAC-Development 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.
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You should have received a copy of the GNU Lesser General Public License along with CPAC-Development. If not, see <https://www.gnu.org/licenses/>. -->
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C-PAC version deprecation scripts
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=================================
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In the rare occasion a version of C-PAC that exists on Docker Hub needs to be deprecated, the files in this directory can facilitate the process.
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See https://fcp-indi.github.io/docs/nightly/developer/deprecating and the individual executable scripts for more information.
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‎deprecate/bash.bashrc‎

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# System-wide .bashrc file for interactive bash(1) shells.
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# Bash is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
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# To enable the settings / commands in this file for login shells as well,
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# this file has to be sourced in /etc/profile.
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# If not running interactively, don't do anything
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[ -z "$PS1" ] && return
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# check the window size after each command and, if necessary,
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# update the values of LINES and COLUMNS.
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shopt -s checkwinsize
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# set variable identifying the chroot you work in (used in the prompt below)
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if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
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debian_chroot=$(cat /etc/debian_chroot)
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fi
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# set a fancy prompt (non-color, overwrite the one in /etc/profile)
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# but only if not SUDOing and have SUDO_PS1 set; then assume smart user.
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if ! [ -n "${SUDO_USER}" -a -n "${SUDO_PS1}" ]; then
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PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
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fi
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# Commented out, don't overwrite xterm -T "title" -n "icontitle" by default.
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# If this is an xterm set the title to user@host:dir
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#case "$TERM" in
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#xterm*|rxvt*)
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# PROMPT_COMMAND='echo -ne "\033]0;${USER}@${HOSTNAME}: ${PWD}\007"'
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# ;;
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#*)
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# ;;
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#esac
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# enable bash completion in interactive shells
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#if ! shopt -oq posix; then
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# if [ -f /usr/share/bash-completion/bash_completion ]; then
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# . /usr/share/bash-completion/bash_completion
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# elif [ -f /etc/bash_completion ]; then
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# . /etc/bash_completion
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# fi
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#fi
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# sudo hint
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if [ ! -e "$HOME/.sudo_as_admin_successful" ] && [ ! -e "$HOME/.hushlogin" ] ; then
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case " $(groups) " in *\ admin\ *|*\ sudo\ *)
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if [ -x /usr/bin/sudo ]; then
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cat <<-EOF
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To run a command as administrator (user "root"), use "sudo <command>".
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See "man sudo_root" for details.
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EOF
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fi
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esac
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fi
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# if the command-not-found package is installed, use it
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if [ -x /usr/lib/command-not-found -o -x /usr/share/command-not-found/command-not-found ]; then
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function command_not_found_handle {
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# check because c-n-f could've been removed in the meantime
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if [ -x /usr/lib/command-not-found ]; then
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/usr/lib/command-not-found -- "$1"
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return $?
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elif [ -x /usr/share/command-not-found/command-not-found ]; then
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/usr/share/command-not-found/command-not-found -- "$1"
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return $?
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else
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printf "%s: command not found\n" "$1" >&2
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return 127
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fi
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}
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fi
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# Display CRITICAL ALERT on launch
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grep -v '^\.\. ' /CRITICAL_ALERT.rst

‎deprecate/build_and_deprecate‎

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# This script takes a tag ($TAG) from https://hub.docker.com/repository/docker/fcpindi/c-pac/tags, and does the following:
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# 1. creates an image tagged ${TAG}-DEPRECATED with the same contents as the given tag except also printing the text in `CRITICAL_ALERT.rst` when the image is run and adding a copy to the log directory of each run generated by the image,
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# 2. replaces that tag with an image that only prints the text in `CRITICAL_ALERT.rst`, and
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# 3. pushes both images to Docker Hub, overwriting any existing images with the same name.
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#
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# Usage: ./build_and_deprecate $DEPRECATED_TAG $RECOMMENDED_MINIMUM_VERSION
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# See https://fcp-indi.github.io/docs/developer/deprecating for more information
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#
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# Copyright (C) 2022 C-PAC Developers
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# This file is part of CPAC-Development.
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# CPAC-Development 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.
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# CPAC-Development 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.
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# You should have received a copy of the GNU Lesser General Public License along with CPAC-Development. If not, see <https://www.gnu.org/licenses/>.
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if [[ $# != 2 ]]
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then
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head -n 7 $(basename "$0")
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exit 0
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fi
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export DEPRECATED_TAG=$1
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export RECOMMENDED_MINIMUM_VERSION=$2
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docker pull fcpindi/c-pac:${DEPRECATED_TAG}
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docker build -t fcpindi/c-pac:${DEPRECATED_TAG}-DEPRECATED --build-arg DEPRECATED_VERSION=${DEPRECATED_TAG} --build-arg RECOMMENDED_MINIMUM_VERSION=${RECOMMENDED_MINIMUM_VERSION} .
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docker build -t fcpindi/c-pac:${DEPRECATED_TAG} -f DEPRECATED.Dockerfile --build-arg DEPRECATED_VERSION=${DEPRECATED_TAG} --build-arg RECOMMENDED_MINIMUM_VERSION=${RECOMMENDED_MINIMUM_VERSION} .
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docker push fcpindi/c-pac:${DEPRECATED_TAG}-DEPRECATED
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docker push fcpindi/c-pac:${DEPRECATED_TAG}

‎deprecate/entrypoint‎

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#!/usr/bin/env bash
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# Copyright (C) 2022 C-PAC Developers
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#
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# This file is part of CPAC-Development.
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#
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# CPAC-Development 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.
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#
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# CPAC-Development 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.
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#
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# You should have received a copy of the GNU Lesser General Public License along with CPAC-Development. If not, see <https://www.gnu.org/licenses/>.
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grep -v '^\.\. ' /CRITICAL_ALERT.rst

‎deprecate/rebuild_and_deprecate‎

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# This script takes a tag ($TAG) from https://hub.docker.com/repository/docker/fcpindi/c-pac/tags, and does the following:
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# 1. recreates an image with the same contents as ${TAG}-DEPRECATED except also printing the text in `CRITICAL_ALERT.rst` when the image is run and adding a copy to the log directory of each run generated by the image,
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# 2. replaces that tag with an image that only prints the text in `CRITICAL_ALERT.rst`, and
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# 3. pushes both images to Docker Hub, overwriting any existing images with the same name.
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#
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# Usage: ./rebuild_and_deprecate $DEPRECATED_TAG $RECOMMENDED_MINIMUM_VERSION
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# See https://fcp-indi.github.io/docs/developer/deprecating for more information
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#
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# Copyright (C) 2022 C-PAC Developers
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# This file is part of CPAC-Development.
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# CPAC-Development 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.
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# CPAC-Development 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.
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# You should have received a copy of the GNU Lesser General Public License along with CPAC-Development. If not, see <https://www.gnu.org/licenses/>.
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if [[ $# != 2 ]]
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then
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head -n 7 $(basename "$0")
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exit 0
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fi
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export DEPRECATED_TAG=$1
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export RECOMMENDED_MINIMUM_VERSION=$2
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docker pull fcpindi/c-pac:${DEPRECATED_TAG}-DEPRECATED
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docker build -t fcpindi/c-pac:${DEPRECATED_TAG}-DEPRECATED --build-arg DEPRECATED_VERSION=${DEPRECATED_TAG} --build-arg RECOMMENDED_MINIMUM_VERSION=${RECOMMENDED_MINIMUM_VERSION} -f redeprecate.Dockerfile .
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docker build -t fcpindi/c-pac:${DEPRECATED_TAG} -f DEPRECATED.Dockerfile --build-arg DEPRECATED_VERSION=${DEPRECATED_TAG} --build-arg RECOMMENDED_MINIMUM_VERSION=${RECOMMENDED_MINIMUM_VERSION} .
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docker push fcpindi/c-pac:${DEPRECATED_TAG}-DEPRECATED
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docker push fcpindi/c-pac:${DEPRECATED_TAG}

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