chore: update dependencies, align with fmriprep

Author: mgxd

Dockerfile

@@ -26,12 +26,10 @@
 ARG BASE_IMAGE=ubuntu:jammy-20240405
 
 # NiBabies wheel
-FROM python:slim AS src
-RUN pip install build
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends git
+FROM ghcr.io/astral-sh/uv:python3.12-alpine AS src
+RUN apk add git
 COPY . /src
-RUN python -m build /src
+RUN uvx --from build pyproject-build --installer uv -w /src
 
 # Older Python to support legacy MCRIBS
 FROM python:3.6.15-slim as pyenv
@@ -54,7 +52,7 @@ FROM downloader as afni
 # The download link can point to newer releases
 # As a safeguard, take advantage of Docker caching, and
 # Bump the date to current to update AFNI
-RUN echo "2023.06.09"
+RUN echo "2025.06.12"
 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 \
@@ -72,22 +70,6 @@ RUN mkdir -p /opt/afni-latest \
         -name "3dAutomask" -or \
         -name "3dvolreg" \) -delete
 
-# ANTs 2.5.4
-FROM downloader as ants
-RUN mkdir -p /opt && \
-    curl -sSLO "https://github.com/ANTsX/ANTs/releases/download/v2.5.4/ants-2.5.4-ubuntu-22.04-X64-gcc.zip" && \
-    unzip ants-2.5.4-ubuntu-22.04-X64-gcc.zip -d /opt && \
-    rm ants-2.5.4-ubuntu-22.04-X64-gcc.zip
-
-# Connectome Workbench 1.5.0
-FROM downloader as workbench
-RUN mkdir /opt/workbench && \
-    curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
-    unzip workbench-linux64-v1.5.0.zip -d /opt && \
-    rm workbench-linux64-v1.5.0.zip && \
-    rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
-    strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
-
 # Micromamba
 FROM downloader as micromamba
 
@@ -99,7 +81,7 @@ RUN apt-get update && \
 
 WORKDIR /
 # Bump the date to current to force update micromamba
-RUN echo "2024.04.25" && curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+RUN echo "2025.06.12" && curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 COPY env.yml /tmp/env.yml
 COPY requirements.txt /tmp/requirements.txt
@@ -180,23 +162,12 @@ RUN apt-get update -qq \
     && ldconfig
 
 COPY --from=afni /opt/afni-latest /opt/afni-latest
-COPY --from=ants /opt/ants-2.5.4 /opt/ants
-COPY --from=workbench /opt/workbench /opt/workbench
 
 # AFNI config
 ENV PATH="/opt/afni-latest:$PATH" \
     AFNI_IMSAVE_WARNINGS="NO" \
     AFNI_PLUGINPATH="/opt/afni-latest"
 
-# ANTs config
-ENV ANTSPATH="/opt/ants" \
-    PATH="/opt/ants/bin:$PATH" \
-    LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
-
-# Workbench config
-ENV PATH="/opt/workbench/bin_linux64:$PATH" \
-    LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
-
 # Install FreeSurfer (with Infant Module)
 COPY --from=nipreps/freesurfer@sha256:3b895fc732a7080374a15c4f976510f39c0c48dc76c030ab27316febd5e419ee /opt/freesurfer /opt/freesurfer
 ENV FREESURFER_HOME="/opt/freesurfer"
@@ -278,8 +249,8 @@ ARG BUILD_DATE
 ARG VCS_REF
 ARG VERSION
 LABEL org.label-schema.build-date=$BUILD_DATE \
-      org.label-schema.name="NiBabies" \
-      org.label-schema.description="NiBabies - NeuroImaging tools for babies" \
+      org.label-schema.name="fMRIPrep Lifespan" \
+      org.label-schema.description="fMRIPrep Lifespan - fMRI processing tool from birth and on" \
       org.label-schema.url="https://github.com/nipreps/nibabies" \
       org.label-schema.vcs-ref=$VCS_REF \
       org.label-schema.vcs-url="https://github.com/nipreps/nibabies" \

env.yml

@@ -1,44 +1,46 @@
 name: nibabies
 channels:
-  - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
-  - conda-forge
-# Update this ~yearly; last updated April 2023
+- https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
+- conda-forge
+# Update this ~yearly; last updated June 12 2025
 dependencies:
-  - python =3.11
-  # Needed for svgo and bids-validator; consider moving to deno
-  - nodejs=20
-  # Intel Math Kernel Library for numpy
-  - mkl=2023.2.0
-  - mkl-service=2.4.0
-  # git-annex for templateflow users with DataLad superdatasets
-  - git-annex=*=alldep*
-  # Base scientific python stack; required by FSL, so pinned here
-  - numpy=1.26
-  - scipy=1.11
-  - matplotlib=3.8
-  - pandas=2.2
-  - h5py=3.10
-  # Dependencies compiled against numpy, best to stick with conda
-  - nitime=0.10
-  - scikit-image=0.22
-  - scikit-learn=1.4
-  # Utilities
-  - graphviz=9.0
-  - pandoc=3.1
-  # Workflow dependencies: ANTs
-  - ants=2.5
-  # Workflow dependencies: Convert3d
-  - convert3d=1.4
-  # Workflow dependencies: FSL (versions pinned in 6.0.7.7)
-  - fsl-bet2=2111.4
-  - fsl-flirt=2111.2
-  - fsl-fast4=2111.3
-  - fsl-fugue=2201.4
-  - fsl-mcflirt=2111.0
-  - fsl-miscmaths=2203.2
-  - fsl-topup=2203.2
-  - pip
-  - pip:
-    - -r requirements.txt
+- python=3.13
+# Needed for svgo and bids-validator; consider moving to deno
+- nodejs=20
+# Intel Math Kernel Library for numpy
+- mkl=2024.2.2
+- mkl-service=2.4.2
+# git-annex for templateflow users with DataLad superdatasets
+- git-annex=*=alldep*
+# Base scientific python stack; required by FSL, so pinned here
+- numpy=2.3
+- scipy=1.15
+- matplotlib=3.10
+- pandas=2.3
+- h5py=3.14
+# Dependencies compiled against numpy, best to stick with conda
+- nitime=0.11
+- scikit-image=0.25
+- scikit-learn=1.7
+# Utilities
+- graphviz=12.2
+- pandoc=3.7
+# Workflow dependencies: ANTs
+- ants=2.6
+# Workflow dependencies: Connectome Workbench
+- connectome-workbench-cli=2.0
+# Workflow dependencies: Convert3d
+- convert3d=1.4
+# Workflow dependencies: FSL (versions pinned in 6.0.7.17.20250415.fe1c582e)
+- fsl-bet2=2111.8
+- fsl-flirt=2111.4
+- fsl-fast4=2111.3
+- fsl-fugue=2201.5
+- fsl-mcflirt=2111.0
+- fsl-miscmaths=2412.4
+- fsl-topup=2203.5
+- pip
+- pip:
+  - -r requirements.txt
 variables:
   FSLOUTPUTTYPE: NIFTI_GZ

wrapper/src/nibabies_wrapper/__main__.py

@@ -29,7 +29,7 @@
 MISSING = """
 Image '{}' is missing
 Would you like to download? [Y/n] """
-PKG_PATH = '/opt/conda/envs/nibabies/lib/python3.11/site-packages'
+PKG_PATH = '/opt/conda/envs/nibabies/lib/python3.13/site-packages'
 TF_TEMPLATES = (
     'MNI152Lin',
     'MNI152NLin2009cAsym',