Merge pull request #1887 from FCP-INDI/develop

Release v1.8.5 Develop branch to Main

Author: sgiavasis

.circleci/main.yml

@@ -157,7 +157,7 @@ commands:
           name: Testing Singularity installation
           command: |
             pip install -r dev/circleci_data/requirements.txt
-            coverage run -m pytest --junitxml=test-results/junit.xml --continue-on-collection-errors  dev/circleci_data/test_install.py
+            coverage run -m pytest --junitxml=test-results/junit.xml --continue-on-collection-errors dev/circleci_data/test_install.py
 
 jobs:
   combine-coverage:

.github/Dockerfiles/AFNI.16.2.07.neurodocker-xenial.Dockerfile

@@ -24,6 +24,7 @@ RUN apt-get update && \
 FROM ghcr.io/fcp-indi/c-pac/ubuntu:xenial-20200114
 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 AFNI 16.2.07 stage"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root
 
 COPY --from=AFNI /opt/afni-latest/ /usr/lib/afni/bin/

.github/Dockerfiles/AFNI.20.0.04-bionic.Dockerfile

@@ -1,6 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free
-LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
-AFNI @update.afni.binaries stage"
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free as AFNI
 USER root
 
 # install AFNI
@@ -21,7 +19,7 @@ RUN if [ -f /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0]; then \
     LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH && \
     export LD_LIBRARY_PATH && \
     apt-get update && apt-get install -y libglw1-mesa-dev && \
-    AFNI_VERSION="20.0.04" && \
+    AFNI_VERSION="21.1.00" && \
     curl -LOJ https://github.com/afni/afni/archive/AFNI_${AFNI_VERSION}.tar.gz && \
     mkdir /opt/afni && \
     tar -xvf afni-AFNI_${AFNI_VERSION}.tar.gz -C /opt/afni --strip-components 1 && \
@@ -49,5 +47,12 @@ RUN apt-get clean && \
     apt-get autoremove -y && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-# set user
-USER c-pac_user
+FROM scratch
+LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+AFNI 21.1.00 (Domitian) stage"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+COPY --from=AFNI /lib/x86_64-linux-gnu/ld* /lib/x86_64-linux-gnu/
+COPY --from=AFNI /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
+COPY --from=AFNI /lib64/ld* /lib64/
+COPY --from=AFNI /opt/afni/ /opt/afni/
+COPY --from=AFNI /usr/lib/x86_64-linux-gnu/lib*so* /usr/lib/x86_64-linux-gnu/

.github/Dockerfiles/AFNI.update.afni.binaries-bionic.Dockerfile renamed to .github/Dockerfiles/AFNI.21.1.00-bionic.Dockerfile

@@ -1,6 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free
-LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
-ANTs 2.2.0 stage"
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free as ANTs
 USER root
 
 # install ANTs from Neurodocker
@@ -42,5 +40,9 @@ RUN apt-get clean && \
     apt-get autoremove -y && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-# set user
-USER c-pac_user
+FROM scratch
+LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+ANTs 2.2.0 stage"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+COPY --from=ANTs /usr/lib/ants/ /usr/lib/ants/
+COPY --from=ANTs /ants_template /ants_template

.github/Dockerfiles/ANTs.2.2.0.neurodocker-bionic.Dockerfile

@@ -37,9 +37,7 @@ RUN apt-get clean && \
 FROM scratch
 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 ANTs 2.3.4 stage"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 COPY --from=ANTs /usr/lib/ants/ /usr/lib/ants/
 COPY --from=ANTs /ants_template /ants_template
 COPY --from=ANTS /etc/locale.gen /etc/locale.gen
-
-# set user
-USER c-pac_user

.github/Dockerfiles/ANTs.2.3.4.neurodocker-xenial.Dockerfile

@@ -1,9 +1,9 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.4
+FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.5
 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/docker_data/default_pipeline.yml /cpac_resources/default_pipeline.yml
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
 RUN pip install -e /code

.github/Dockerfiles/ANTs.2.3.5-bionic.Dockerfile

@@ -1,9 +1,9 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.4
+FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.5
 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/docker_data/default_pipeline.yml /cpac_resources/default_pipeline.yml
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
 RUN pip install -e /code

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

@@ -1,9 +1,9 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.4
+FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.5
 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/docker_data/default_pipeline.yml /cpac_resources/default_pipeline.yml
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
 RUN pip install -e /code