From 400d8c1fcda61ee32d8da25c4a3cbcb13ab430d0 Mon Sep 17 00:00:00 2001 From: Jon Cluce Date: Thu, 12 Dec 2024 10:02:49 -0500 Subject: [PATCH] :pencil2: Fix repeated `.dev3` --- .../C-PAC.develop-ABCD-HCP-bionic.Dockerfile | 33 ----------------- ...PAC.develop-fMRIPrep-LTS-xenial.Dockerfile | 35 ------------------- .../C-PAC.develop-jammy.Dockerfile | 2 +- .../C-PAC.develop-lite-jammy.Dockerfile | 2 +- .github/Dockerfiles/base-standard.Dockerfile | 2 +- Dockerfile | 2 +- variant-ABCD-HCP.Dockerfile | 33 ----------------- variant-fMRIPrep-LTS.Dockerfile | 35 ------------------- variant-lite.Dockerfile | 2 +- 9 files changed, 5 insertions(+), 141 deletions(-) delete mode 100644 .github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile delete mode 100644 .github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile delete mode 100644 variant-ABCD-HCP.Dockerfile delete mode 100644 variant-fMRIPrep-LTS.Dockerfile diff --git a/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile b/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile deleted file mode 100644 index 1114ae5da..000000000 --- a/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile +++ /dev/null @@ -1,33 +0,0 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.post1.dev3.dev3.dev3 -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 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 && \ - chmod +x /code/run-with-freesurfer.sh -ENTRYPOINT ["/code/run-with-freesurfer.sh"] - -# Link libraries for Singularity images -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 diff --git a/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile b/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile deleted file mode 100644 index 824bbf672..000000000 --- a/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile +++ /dev/null @@ -1,35 +0,0 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.post1.dev3.dev3.dev3 -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 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 && \ - 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/* /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 diff --git a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile index 3bcfdf79c..6de7379c1 100644 --- a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3 LABEL org.opencontainers.image.description "Full C-PAC image" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile index a3b38ee24..98d4ed9f8 100644 --- a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3 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 diff --git a/.github/Dockerfiles/base-standard.Dockerfile b/.github/Dockerfiles/base-standard.Dockerfile index c01e250dc..2a448e118 100644 --- a/.github/Dockerfiles/base-standard.Dockerfile +++ b/.github/Dockerfiles/base-standard.Dockerfile @@ -16,7 +16,7 @@ # License along with C-PAC. If not, see . FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-jammy as FreeSurfer -FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \ Standard software dependencies for C-PAC standard images" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC diff --git a/Dockerfile b/Dockerfile index 3bcfdf79c..6de7379c1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3 LABEL org.opencontainers.image.description "Full C-PAC image" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/variant-ABCD-HCP.Dockerfile b/variant-ABCD-HCP.Dockerfile deleted file mode 100644 index 1114ae5da..000000000 --- a/variant-ABCD-HCP.Dockerfile +++ /dev/null @@ -1,33 +0,0 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.post1.dev3.dev3.dev3 -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 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 && \ - chmod +x /code/run-with-freesurfer.sh -ENTRYPOINT ["/code/run-with-freesurfer.sh"] - -# Link libraries for Singularity images -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 diff --git a/variant-fMRIPrep-LTS.Dockerfile b/variant-fMRIPrep-LTS.Dockerfile deleted file mode 100644 index 824bbf672..000000000 --- a/variant-fMRIPrep-LTS.Dockerfile +++ /dev/null @@ -1,35 +0,0 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.post1.dev3.dev3.dev3 -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 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 && \ - 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/* /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 diff --git a/variant-lite.Dockerfile b/variant-lite.Dockerfile index a3b38ee24..98d4ed9f8 100644 --- a/variant-lite.Dockerfile +++ b/variant-lite.Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3 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