chore: Relax dependencies to numpy 2.0 compatibility

.circleci/config.yml

@@ -10,33 +10,19 @@ jobs:
 
     steps:
       - checkout
-      - restore_cache:
-          keys:
-            - env-v6-{{ .Branch }}-
-            - env-v6-master-
-            - env-v6-
+      - run:
+          name: Ensure uv is present
+          command: uv -V || curl -LsSf https://astral.sh/uv/install.sh | sh
       - run:
           name: Setup git-annex
           command: |
-              sudo apt update && sudo apt-get install apt-transport-https ca-certificates -y && sudo update-ca-certificates
-              if [[ ! -d /opt/circleci/git-annex.linux ]]; then
-                cd /tmp
-                wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
-                tar xzf git-annex-standalone-amd64.tar.gz -C /opt/circleci/
-              fi
+              uv tool install git-annex
               git config --global user.name 'NiPy'
               git config --global user.email '[email protected]'
       - run:
           name: Setup DataLad
           command: |
-              python3 -m pip install --no-cache-dir -U pip "setuptools >= 45.0" "setuptools_scm[toml] >= 6.2"
-              python3 -m pip install --no-cache-dir -U datalad datalad-osf
-
-      - save_cache:
-          key: env-v6-{{ .Branch }}-{{ .BuildNum }}
-          paths:
-            - /opt/circleci/git-annex.linux
-            - /opt/circleci/.pyenv/versions
+              uv tool install --with-executables-from=datalad-osf,datalad-next datalad
 
       - restore_cache:
           keys:
@@ -46,9 +32,6 @@ jobs:
       - run:
           name: Install test data from GIN
           command: |
-              export PATH=/opt/circleci/git-annex.linux:$PATH
-              pyenv local 3
-              eval "$(pyenv init --path)"
               mkdir -p /tmp/data
               cd /tmp/data
               datalad install -r https://gin.g-node.org/oesteban/nitransforms-tests
@@ -61,10 +44,10 @@ jobs:
 
       - restore_cache:
           keys:
-            - build-v1-{{ .Branch }}-{{ epoch }}
-            - build-v1-{{ .Branch }}-
-            - build-v1-master-
-            - build-v1-
+            - build-v2-{{ .Branch }}-{{ epoch }}
+            - build-v2-{{ .Branch }}-
+            - build-v2-master-
+            - build-v2-
           paths:
             - /tmp/docker
       - run:
@@ -81,13 +64,13 @@ jobs:
               set -e
               if [[ "$success" = "0" ]]; then
                   echo "Pulling from local registry"
-                  docker tag localhost:5000/ubuntu ubuntu:xenial-20200114
+                  docker tag localhost:5000/ubuntu ubuntu:jammy-20250730
                   docker pull localhost:5000/nitransforms
                   docker tag localhost:5000/nitransforms nitransforms:latest
               else
                   echo "Pulling from Docker Hub"
-                  docker pull ubuntu:xenial-20200114
-                  docker tag ubuntu:xenial-20200114 localhost:5000/ubuntu
+                  docker pull ubuntu:jammy-20250730
+                  docker tag ubuntu:jammy-20250730 localhost:5000/ubuntu
                   docker push localhost:5000/ubuntu
               fi
       - run:
@@ -99,7 +82,7 @@ jobs:
                   -t nitransforms:latest \
                   --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                   --build-arg VCS_REF=`git rev-parse --short HEAD` \
-                  --build-arg VERSION=$( python3 -m setuptools_scm ) . \
+                  --build-arg VERSION=$( uv run --no-project -w setuptools_scm -m setuptools_scm ) . \
                   && e=0 && break || sleep 15
               done && [ "$e" -eq "0" ]
               docker tag nitransforms:latest localhost:5000/nitransforms
@@ -110,13 +93,13 @@ jobs:
               docker exec -it registry /bin/registry garbage-collect --delete-untagged \
                   /etc/docker/registry/config.yml
       - save_cache:
-          key: build-v1-{{ .Branch }}-{{ epoch }}
+          key: build-v2-{{ .Branch }}-{{ epoch }}
           paths:
             - /tmp/docker
       - run:
           name: Check version packaged in Docker image
           command: |
-              THISVERSION=${CIRCLE_TAG:-$(python3 -m setuptools_scm)}
+              THISVERSION=${CIRCLE_TAG:-$( uv run --no-project -w setuptools_scm -m setuptools_scm )}
               INSTALLED_VERSION=$(\
                 docker run -it --rm --entrypoint=python nitransforms \
                     -c 'import nitransforms as nit; print(nit.__version__, end="")' )
@@ -141,10 +124,11 @@ jobs:
               -w /src/nitransforms -v $PWD:/src/nitransforms \
               -v /tmp/data/nitransforms-tests:/data -e TEST_DATA_HOME=/data \
               -e COVERAGE_FILE=/tmp/coverage/.pytest.coverage \
-              -v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro \
+              -v /tmp/fslicense/license.txt:/usr/local/freesurfer/license.txt:ro \
               -v /tmp/tests:/tmp nitransforms:latest \
               pytest --junit-xml=/tmp/summaries/pytest.xml \
                      --cov nitransforms --cov-report xml:/tmp/coverage/unittests.xml \
+                     -n auto \
                      nitransforms/
       - run:
           name: Submit unit test coverage

Dockerfile

@@ -1,24 +1,22 @@
 # Ubuntu 22.04 LTS - Jammy
-ARG BASE_IMAGE=ubuntu:jammy-20240125
+ARG BASE_IMAGE=ubuntu:jammy-20250730
 
 #
 # Build 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:python3.13-alpine AS src
+RUN apk add git
 COPY . /src
-RUN python -m build /src
+RUN uv build --wheel /src
 
 #
 # Download stages
 #
 
 # Utilities for downloading packages
-FROM ${BASE_IMAGE} as downloader
+FROM ${BASE_IMAGE} AS downloader
 # Bump the date to current to refresh curl/certificates/etc
-RUN echo "2023.07.20"
+RUN echo "2025.09.25"
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     binutils \
@@ -30,159 +28,79 @@ RUN apt-get update && \
 
 RUN update-ca-certificates -f
 
-# FreeSurfer 7.3.2
-FROM downloader as freesurfer
-COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exclude.txt
-COPY docker/files/fs-cert.pem /usr/local/etc/fs-cert.pem
-RUN curl --cacert /usr/local/etc/fs-cert.pem \
-     -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \
-     | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3.2-exclude.txt
-
-# AFNI
-FROM downloader as afni
-# Bump the date to current to update AFNI
-RUN echo "2023.07.20"
-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 \( \
-        -name "3dTshift" -or \
-        -name "3dUnifize" -or \
-        -name "3dAutomask" -or \
-        -name "3dvolreg" -or \
-        -name "3dNwarpApply" \
-    \) -delete
-
 # Micromamba
-FROM downloader as micromamba
-
-# Install a C compiler to build extensions when needed.
-# traits<6.4 wheels are not available for Python 3.11+, but build easily.
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends build-essential && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+FROM downloader AS micromamba
 
 WORKDIR /
 # Bump the date to current to force update micromamba
-RUN echo "2024.02.06"
+RUN echo "2025.09.05"
 RUN 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
 WORKDIR /tmp
 RUN micromamba create -y -f /tmp/env.yml && \
     micromamba clean -y -a
 
 #
 # Main stage
 #
-FROM ${BASE_IMAGE} as nitransforms
+FROM ${BASE_IMAGE} AS nitransforms
 
 # Configure apt
 ENV DEBIAN_FRONTEND="noninteractive" \
     LANG="en_US.UTF-8" \
     LC_ALL="en_US.UTF-8"
 
-# Some baseline tools; bc is needed for FreeSurfer, so don't drop it
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-                    bc \
-                    ca-certificates \
-                    curl \
-                    git \
-                    gnupg \
-                    lsb-release \
-                    netbase \
-                    xvfb && \
+        libexpat1 \
+        libgomp1 \
+        && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-# 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 \
-           gsl-bin \
-           libglib2.0-0 \
-           libglu1-mesa-dev \
-           libglw1-mesa \
-           libgomp1 \
-           libjpeg62 \
-           libpng12-0 \
-           libxm4 \
-           libxp6 \
-           netpbm \
-           tcsh \
-           xfonts-base \
-           xvfb \
-    && 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 \
-    && apt-get install -f \
-    && 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
-
-# Install files from stages
-COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
-COPY --from=afni /opt/afni-latest /opt/afni-latest
+# Install FreeSurfer and AFNI bins from images
+COPY --from=freesurfer/freesurfer:7.4.1 \
+    /usr/local/freesurfer/bin/mri_vol2vol \
+    /usr/local/freesurfer/bin/
+COPY --from=afni/afni_make_build:AFNI_25.2.09 \
+    /opt/afni/install/libf2c.so \
+    /opt/afni/install/libmri.so \
+    /usr/local/lib/
+COPY --from=afni/afni_make_build:AFNI_25.2.09 \
+    /opt/afni/install/3dAllineate \
+    /opt/afni/install/3dNwarpApply \
+    /opt/afni/install/3dWarp \
+    /opt/afni/install/3drefit \
+    /opt/afni/install/3dvolreg \
+    /usr/local/bin/
 
 # Simulate SetUpFreeSurfer.sh
 ENV OS="Linux" \
     FS_OVERRIDE=0 \
     FIX_VERTEX_AREA="" \
     FSF_OUTPUT_FORMAT="nii.gz" \
-    FREESURFER_HOME="/opt/freesurfer"
+    FREESURFER_HOME="/usr/local/freesurfer"
 ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
     FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
-    MNI_DIR="$FREESURFER_HOME/mni" \
     LOCAL_DIR="$FREESURFER_HOME/local" \
-    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
-    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
-    MNI_DATAPATH="$FREESURFER_HOME/mni/data"
-ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
-    MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
-    PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
+    PATH="$FREESURFER_HOME/bin:$PATH"
 
 # AFNI config
-ENV PATH="/opt/afni-latest:$PATH" \
-    AFNI_IMSAVE_WARNINGS="NO" \
-    AFNI_PLUGINPATH="/opt/afni-latest"
-
-# Workbench config
-ENV PATH="/opt/workbench/bin_linux64:$PATH"
+ENV AFNI_IMSAVE_WARNINGS="NO"
 
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users neuro
 WORKDIR /home/neuro
-ENV HOME="/home/neuro" \
-    LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
+ENV HOME="/home/neuro"
 
 COPY --from=micromamba /bin/micromamba /bin/micromamba
 COPY --from=micromamba /opt/conda/envs/nitransforms /opt/conda/envs/nitransforms
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 RUN micromamba shell init -s bash && \
     echo "micromamba activate nitransforms" >> $HOME/.bashrc
-ENV PATH="/opt/conda/envs/nitransforms/bin:$PATH" \
-    CPATH="/opt/conda/envs/nitransforms/include:$CPATH" \
-    LD_LIBRARY_PATH="/opt/conda/envs/nitransforms/lib:$LD_LIBRARY_PATH"
+ENV PATH="/opt/conda/envs/nitransforms/bin:$PATH"
 
 # FSL environment
 ENV LANG="C.UTF-8" \
@@ -196,22 +114,10 @@ ENV LANG="C.UTF-8" \
     FSLREMOTECALL="" \
     FSLGECUDAQ="cuda.q"
 
-# Unless otherwise specified each process should only use one thread - nipype
-# will handle parallelization
-ENV MKL_NUM_THREADS=1 \
-    OMP_NUM_THREADS=1
-
 # Install package
-# CRITICAL: Make sure python setup.py --version has been run at least once
-#           outside the container, with access to the git history.
 COPY --from=src /src/dist/*.whl .
 RUN python -m pip install --no-cache-dir $( ls *.whl )[all]
 
-
-RUN find $HOME -type d -exec chmod go=u {} + && \
-    find $HOME -type f -exec chmod go=u {} + && \
-    rm -rf $HOME/.npm $HOME/.conda $HOME/.empty
-
 RUN ldconfig
 WORKDIR /tmp/