📦 Update main Dockerfiles from develop

Author: shnizzedy

Dockerfile

@@ -1,24 +1,52 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.5.dev
+# 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/>.
+FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.6.dev1
 LABEL org.opencontainers.image.description "Full C-PAC image"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root
 
 # install C-PAC
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
-RUN pip install -e /code
+RUN pip cache purge && pip install -e /code
 # set up runscript
 COPY dev/docker_data /code/docker_data
-RUN rm -Rf /code/docker_data/Dockerfiles && \
+RUN rm -Rf /code/docker_data/checksum && \
     mv /code/docker_data/* /code && \
     rm -Rf /code/docker_data && \
     chmod +x /code/run.py && \
     chmod +x /code/run-with-freesurfer.sh
 ENTRYPOINT ["/code/run-with-freesurfer.sh"]
 
 # link libraries & clean up
-RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
-    ldconfig && \
-    chmod 777 $(ls / | grep -v sys | grep -v proc)
+# link libraries & clean up
+RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
+    && find / -type f -print0 | sort -t/ -k2 | xargs -0 rdfind -makehardlinks true \
+    && rm -rf results.txt \
+    && apt-get remove rdfind -y \
+    && apt-get clean \
+    && apt-get autoremove -y \
+    && ldconfig \
+    && chmod 777 / \
+    && chmod 777 $(ls / | grep -v sys | grep -v proc)
+ENV PYTHONUSERBASE=/home/c-pac_user/.local
+ENV PATH=$PATH:/home/c-pac_user/.local/bin \
+    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
 
 # set user
+WORKDIR /home/c-pac_user
 # USER c-pac_user

variant-ABCD-HCP.Dockerfile

@@ -1,26 +1,33 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.5.dev
+FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.6.dev1
 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)"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root
 
 # install C-PAC
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
-RUN pip install -e /code
+RUN pip cache purge && pip install -e /code
 # set up runscript
 COPY dev/docker_data /code/docker_data
-RUN rm -Rf /code/docker_data/Dockerfiles && \
+RUN rm -Rf /code/docker_data/checksum && \
     mv /code/docker_data/* /code && \
     rm -Rf /code/docker_data && \
     chmod +x /code/run.py && \
     chmod +x /code/run-with-freesurfer.sh
 ENTRYPOINT ["/code/run-with-freesurfer.sh"]
 
 # Link libraries for Singularity images
-RUN ldconfig
-
-RUN apt-get clean && \
-    apt-get autoremove -y && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+RUN ldconfig \
+    && apt-get clean \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/pip/* \
+    && chmod 777 / \
+    && chmod -R 777 /home/c-pac_user \
+    && chmod 777 $(ls / | grep -v sys | grep -v proc)
+ENV PYTHONUSERBASE=/home/c-pac_user/.local
+ENV PATH=$PATH:/home/c-pac_user/.local/bin \
+    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
 
 # set user
+WORKDIR /home/c-pac_user
 # USER c-pac_user

variant-fMRIPrep-LTS.Dockerfile

@@ -1,28 +1,35 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.5.dev
+FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.6.dev1
 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)"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root
 
 # install C-PAC & set up runscript
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
-RUN pip install -e /code
+RUN pip cache purge && pip install -e /code
 # set up runscript
 COPY dev/docker_data /code/docker_data
-RUN rm -Rf /code/docker_data/Dockerfiles && \
+RUN rm -Rf /code/docker_data/checksum && \
     mv /code/docker_data/* /code && \
     rm -Rf /code/docker_data && \
     chmod +x /code/run.py && \
     chmod +x /code/run-with-freesurfer.sh
 ENTRYPOINT ["/code/run-with-freesurfer.sh"]
 
 # link libraries & clean up
-RUN sed -i 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
-    locale-gen && \
-    apt-get clean && \
-    apt-get autoremove -y && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
-    ldconfig && \
-    chmod 777 $(ls / | grep -v sys | grep -v proc)
+RUN sed -i 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+    && locale-gen \
+    && apt-get clean \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/pip/* \
+    && ldconfig \
+    && chmod 777 / \
+    && chmod -R 777 /home/c-pac_user \
+    && chmod 777 $(ls / | grep -v sys | grep -v proc)
+ENV PYTHONUSERBASE=/home/c-pac_user/.local
+ENV PATH=$PATH:/home/c-pac_user/.local/bin \
+    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
 
 # set user
+WORKDIR /home/c-pac_user
 # USER c-pac_user

variant-lite.Dockerfile

@@ -1,12 +1,53 @@
-FROM ghcr.io/fcp-indi/c-pac:latest
+# 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/>.
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.6.dev1
 LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root
+
+# install C-PAC
+COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
+COPY . /code
+COPY --from=ghcr.io/fcp-indi/c-pac_templates:latest /cpac_templates /cpac_templates
+RUN pip cache purge && pip install -e /code
+# set up runscript
+COPY dev/docker_data /code/docker_data
+RUN rm -Rf /code/docker_data/checksum && \
+    mv /code/docker_data/* /code && \
+    rm -Rf /code/docker_data && \
+    chmod +x /code/run.py && \
+    rm -Rf /code/run-with-freesurfer.sh
 ENTRYPOINT ["/code/run.py"]
 
-# remove FreeSurfer, link libraries & clean up
-RUN rm -rf /usr/lib/freesurfer/ /code/run-with-freesurfer.sh /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
-    ln -svf /usr/lib/x86_64-linux-gnu/libgsl.so.23 /usr/lib/x86_64-linux-gnu/libgsl.so.0 && ldconfig && \
-    chmod 777 $(ls / | grep -v sys | grep -v proc)
+# link libraries & clean up
+# link libraries & clean up
+RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
+    && find / -type f -print0 | sort -t/ -k2 | xargs -0 rdfind -makehardlinks true \
+    && rm -rf results.txt \
+    && apt-get remove rdfind -y \
+    && apt-get clean \
+    && apt-get autoremove -y \
+    && ldconfig \
+    && chmod 777 / \
+    && chmod 777 $(ls / | grep -v sys | grep -v proc)
+ENV PYTHONUSERBASE=/home/c-pac_user/.local
+ENV PATH=$PATH:/home/c-pac_user/.local/bin \
+    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
 
 # set user
+WORKDIR /home/c-pac_user
 # USER c-pac_user