Merge pull request #290 from nipreps/mnt/drop-templateflow-patches

MNT: Drop templateflow patches after smriprep changes

Author: mgxd

.circleci/bcp_anat_outputs.txt

@@ -26,16 +26,16 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_smoothwm.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_smoothwm.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-WM_probseg.nii.gz

.circleci/bcp_full_outputs.txt

@@ -26,16 +26,16 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_smoothwm.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_smoothwm.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-WM_probseg.nii.gz

.circleci/config.yml

@@ -95,45 +95,8 @@ jobs:
       - run: *docker_auth
       - run: *setup_docker_registry
       - run:
-          name: Save Docker registry
-          command: |
-            if [[ ! -f /tmp/images/registry.tar.gz ]]; then
-              mkdir -p /tmp/images
-              docker save registry:2 | gzip > /tmp/images/registry.tar.gz
-            fi
-      - run:
-          name: Pull base image (ubuntu:focal)
-          command: |
-            set +e
-            docker pull localhost:5000/ubuntu
-            success=$?
-            set -e
-            if [[ "$success" = "0" ]]; then
-                echo "Pulling from local registry"
-                docker tag localhost:5000/ubuntu ubuntu:focal
-            else
-                echo "Pulling from Docker Hub"
-                docker pull ubuntu:focal
-                docker tag ubuntu:focal localhost:5000/ubuntu
-                docker push localhost:5000/ubuntu
-            fi
-      - run:
-          name: Pull nibabies image (nipreps/nibabies)
-          command: |
-            set +e
-            docker pull localhost:5000/nibabies
-            success=$?
-            set -e
-            if [[ "$success" = "0" ]]; then
-                echo "Pulled from local registry"
-                docker tag localhost:5000/nibabies nipreps/nibabies:dev
-                docker tag localhost:5000/nibabies nipreps/nibabies
-            else
-                echo "Pulling unstable from Docker Hub"
-                docker pull nipreps/nibabies:unstable
-                docker tag nipreps/nibabies:unstable nipreps/nibabies:dev
-                docker tag nipreps/nibabies:unstable nipreps/nibabies
-            fi
+          name: Create Docker builder
+          command: docker buildx create --use --name=builder --driver=docker-container
       - run:
           name: Clean and check images (before build)
           command: |
@@ -155,15 +118,13 @@ jobs:
               echo "them to your fork with ``git push origin --tags``"
             fi
             # Build docker image
-            e=1 && for i in {1..3}; do
-              docker build --rm \
-                --cache-from=nipreps/nibabies:dev \
+            docker buildx build --load --builder builder \
+                --cache-from localhost:5000/nibabies \
+                --cache-from nipreps/nibabies:dev \
                 -t nipreps/nibabies:dev \
                 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                 --build-arg VCS_REF=`git rev-parse --short HEAD` \
-                --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
-              && e=0 && break || sleep 15
-            done && [ "$e" -eq "0" ]
+                --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" .
       - run:
           name: Check Docker images (after build)
           command: docker images

Dockerfile

@@ -51,7 +51,14 @@ RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_6
 RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
     && echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list
 
-# # AFNI latest (neurodocker build)
+# AFNI 2023.04.04
+# Configure PPAs for libpng12 and libxp6
+RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
+    && GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \
+    && echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \
+    && echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list
+
+# Dependencies for AFNI; requires a discontinued multiarch-support package from bionic (18.04)
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            ed \
@@ -63,35 +70,31 @@ RUN apt-get update -qq \
            libjpeg62 \
            libpng12-0 \
            libxm4 \
+           libxp6 \
            netpbm \
            tcsh \
            xfonts-base \
            xvfb \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
     && curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \
     && dpkg -i /tmp/multiarch.deb \
     && rm /tmp/multiarch.deb \
-    && curl -sSL --retry 5 -o /tmp/libxp6.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
-    && dpkg -i /tmp/libxp6.deb \
-    && rm /tmp/libxp6.deb \
     && apt-get install -f \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
+    && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
     && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
     && if [ -n "$gsl2_path" ]; then \
          ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
     fi \
-    && ldconfig \
-    && echo "Downloading AFNI ..." \
-    && mkdir -p /opt/afni-latest \
+    && ldconfig
+
+RUN mkdir -p /opt/afni-latest \
     && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
     | tar -xz -C /opt/afni-latest --strip-components 1 \
     --exclude "linux_openmp_64/*.gz" \
     --exclude "linux_openmp_64/funstuff" \
     --exclude "linux_openmp_64/shiny" \
     --exclude "linux_openmp_64/afnipy" \
     --exclude "linux_openmp_64/lib/RetroTS" \
+    --exclude "linux_openmp_64/lib_RetroTS" \
     --exclude "linux_openmp_64/meica.libs" \
     # Keep only what we use
     && find /opt/afni-latest -type f -not \( \

nibabies/utils/patches.py

@@ -83,10 +83,10 @@ def init_infant_anat_wf(
         GIFTI surfaces (gray/white boundary, midthickness, pial, inflated)
     """
     from nipype.interfaces.ants.base import Info as ANTsInfo
+    from smriprep.workflows.norm import init_anat_norm_wf
 
     from ...utils.misc import fix_multi_source_name
     from .brain_extraction import init_infant_brain_extraction_wf
-    from .norm import init_anat_norm_wf
     from .outputs import (
         init_anat_derivatives_wf,
         init_anat_reports_wf,