Revert "chore: Use pixi to manage test environment"

.dockerignore

@@ -12,7 +12,3 @@ fmriprep.egg-info/**/*
 fmriprep.egg-info
 .eggs/**/*
 .eggs
-
-.venv
-.pixi
-.tox

Dockerfile

@@ -22,79 +22,226 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-ARG BASE_IMAGE=ghcr.io/nipreps/fmriprep-base:20251006
+# Ubuntu 22.04 LTS - Jammy
+ARG BASE_IMAGE=ubuntu:jammy-20240125
 
 #
-# Build pixi environment
-# The Pixi environment includes:
-#   - Python
-#     - Scientific Python stack (via conda-forge)
-#     - General Python dependencies (via PyPI)
-#   - FSL (via fslconda)
-#   - ants (via conda-forge)
-#   - connectome-workbench (via conda-forge)
-#   - ...
+# Build wheel
 #
-FROM ghcr.io/prefix-dev/pixi:0.53.0 AS build
+FROM python:slim AS src
+RUN pip install build
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends git
+COPY . /src
+RUN python -m build /src
+
+#
+# Download stages
+#
+
+# Utilities for downloading packages
+FROM ${BASE_IMAGE} as downloader
+# Bump the date to current to refresh curl/certificates/etc
+RUN echo "2024.03.08"
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
+                    binutils \
+                    bzip2 \
                     ca-certificates \
-                    git && \
+                    curl \
+                    unzip && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-# Run post-link scripts during install, but use global to keep out of source tree
-RUN pixi config set --global run-post-link-scripts insecure
-
-# Install dependencies before the package itself to leverage caching
-RUN mkdir /app
-COPY pixi.lock pyproject.toml /app
-WORKDIR /app
-RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e niworkflows -e test --frozen --skip niworkflows
-# Note that PATH gets hard-coded. Remove it and re-apply in final image
-RUN pixi shell-hook -e niworkflows --as-is | grep -v PATH > /shell-hook.sh
-RUN pixi shell-hook -e test --as-is | grep -v PATH > /test-shell-hook.sh
-
-# Finally, install the package
-COPY . /app
-RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e niworkflows -e test --frozen
 
-#
-# Pre-fetch templates
-#
-FROM ghcr.io/astral-sh/uv:python3.12-alpine AS templates
-ENV TEMPLATEFLOW_HOME="/templateflow"
-RUN uv pip install --system templateflow
-COPY docker/fetch_templates.py fetch_templates.py
-RUN python fetch_templates.py
+# FreeSurfer 7.3.2
+FROM downloader as freesurfer
+COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exclude.txt
+RUN curl -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 "2024.03.08"
+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 \( \
+        -name "3dTshift" -or \
+        -name "3dUnifize" -or \
+        -name "3dAutomask" -or \
+        -name "3dvolreg" \) -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/*
+
+WORKDIR /
+# Bump the date to current to force update micromamba
+RUN echo "2024.03.08"
+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 base
+FROM ${BASE_IMAGE} as main
+
+# 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 && \
+    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 $gsl2_path)/libgsl.so.0"; \
+    fi \
+    && ldconfig
+
+# Install files from stages
+COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
+COPY --from=afni /opt/afni-latest /opt/afni-latest
+
+# Simulate SetUpFreeSurfer.sh
+ENV OS="Linux" \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA="" \
+    FSF_OUTPUT_FORMAT="nii.gz" \
+    FREESURFER_HOME="/opt/freesurfer"
+ENV SUBJECTS_DIR="$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"
+
+# AFNI config
+ENV PATH="/opt/afni-latest:$PATH" \
+    AFNI_IMSAVE_WARNINGS="NO" \
+    AFNI_PLUGINPATH="/opt/afni-latest"
 
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users niworkflows
 WORKDIR /home/niworkflows
-ENV HOME="/home/niworkflows"
-
-COPY --link --from=templates /templateflow /home/fmriprep/.cache/templateflow
-
-RUN chmod -R go=u $HOME
+ENV HOME="/home/niworkflows" \
+    LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
+
+COPY --from=micromamba /bin/micromamba /bin/micromamba
+COPY --from=micromamba /opt/conda/envs/niworkflows /opt/conda/envs/niworkflows
+
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+RUN micromamba shell init -s bash && \
+    echo "micromamba activate niworkflows" >> $HOME/.bashrc
+ENV PATH="/opt/conda/envs/niworkflows/bin:$PATH" \
+    CPATH="/opt/conda/envs/niworkflows/include:$CPATH" \
+    LD_LIBRARY_PATH="/opt/conda/envs/niworkflows/lib:$LD_LIBRARY_PATH"
+
+COPY docker/fetch_templates.py /tmp/fetch_templates.py
+RUN python /tmp/fetch_templates.py && \
+    rm /tmp/fetch_templates.py && \
+    find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
+    find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
+
+# FSL environment
+ENV LANG="C.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    PYTHONNOUSERSITE=1 \
+    FSLDIR="/opt/conda/envs/fmriprep" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    FSLLOCKDIR="" \
+    FSLMACHINELIST="" \
+    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
 
-COPY docker/files/nipype.cfg /home/niworkflows/.nipype/nipype.cfg
-
-WORKDIR /tmp
+# Installing niworkflows
+COPY --from=src /src/dist/*.whl .
+RUN pip install --no-cache-dir $( ls *.whl )[all]
 
-FROM base AS test
+COPY docker/files/nipype.cfg /home/niworkflows/.nipype/nipype.cfg
 
-COPY --link --from=build /app/.pixi/envs/test /app/.pixi/envs/test
-COPY --link --from=build /test-shell-hook.sh /shell-hook.sh
-RUN cat /shell-hook.sh >> $HOME/.bashrc
-ENV PATH="/app/.pixi/envs/test/bin:$PATH"
+# Cleanup and ensure perms.
+RUN rm -rf $HOME/.npm $HOME/.conda $HOME/.empty && \
+    find $HOME -type d -exec chmod go=u {} + && \
+    find $HOME -type f -exec chmod go=u {} +
 
-ENV FSLDIR="/app/.pixi/envs/test"
+# Final settings
+WORKDIR /tmp
+ARG BUILD_DATE
+ARG VCS_REF
+LABEL org.label-schema.build-date=$BUILD_DATE \
+      org.label-schema.name="niworkflows" \
+      org.label-schema.description="niworkflows - NeuroImaging workflows" \
+      org.label-schema.url="https://github.com/nipreps/niworkflows" \
+      org.label-schema.vcs-ref=$VCS_REF \
+      org.label-schema.vcs-url="https://github.com/nipreps/niworkflows" \
+      org.label-schema.version=$VERSION \
+      org.label-schema.schema-version="1.0"

env.yml

@@ -0,0 +1,36 @@
+name: niworkflows
+channels:
+  - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
+  - conda-forge
+# Update this ~yearly; last updated Mar 2025
+dependencies:
+  - python=3.12
+  # Intel Math Kernel Library for numpy
+  - mkl=2024.2.2
+  - mkl-service=2.4.2
+  # Base scientific python stack; required by FSL, so pinned here
+  - numpy=1.26
+  - scipy=1.15
+  - matplotlib=3.9
+  - pandas=2.2
+  - h5py=3.13
+  # Dependencies compiled against numpy, best to stick with conda
+  - scikit-image=0.25
+  - scikit-learn=1.6
+  # Utilities
+  - graphviz=11.0
+  # Workflow dependencies: ANTs
+  - ants=2.5
+  # 5.4.1 and 5.4.2 cause segfaults with ants
+  # Try to remove this ASAP
+  # https://github.com/conda-forge/ants-feedstock/issues/19
+  - libitk=5.4.0
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.13)
+  - fsl-bet2=2111.8
+  - fsl-flirt=2111.2
+  - fsl-fast4=2111.3
+  - fsl-mcflirt=2111.0
+  - fsl-miscmaths=2203.2
+  - pip
+  - pip:
+    - -r requirements.txt