Merge pull request #990 from effigies/pixi

chore: Use pixi to manage test environment

Author: effigies

.dockerignore

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

Dockerfile

@@ -22,226 +22,79 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-# Ubuntu 22.04 LTS - Jammy
-ARG BASE_IMAGE=ubuntu:jammy-20240125
+ARG BASE_IMAGE=ghcr.io/nipreps/fmriprep-base:20251006
 
 #
-# Build wheel
+# 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)
+#   - ...
 #
-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"
+FROM ghcr.io/prefix-dev/pixi:0.53.0 AS build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-                    binutils \
-                    bzip2 \
                     ca-certificates \
-                    curl \
-                    unzip && \
+                    git && \
     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
 
-# 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
+#
+# 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
 
-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 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"
+FROM ${BASE_IMAGE} AS base
 
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users niworkflows
 WORKDIR /home/niworkflows
-ENV HOME="/home/niworkflows" \
-    LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$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"
+ENV HOME="/home/niworkflows"
+
+COPY --link --from=templates /templateflow /home/fmriprep/.cache/templateflow
+
+RUN chmod -R go=u $HOME
 
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
-# Installing niworkflows
-COPY --from=src /src/dist/*.whl .
-RUN pip install --no-cache-dir $( ls *.whl )[all]
-
 COPY docker/files/nipype.cfg /home/niworkflows/.nipype/nipype.cfg
 
-# Cleanup and ensure perms.
-RUN rm -rf $HOME/.npm $HOME/.conda $HOME/.empty && \
-    find $HOME -type d -exec chmod go=u {} + && \
-    find $HOME -type f -exec chmod go=u {} +
-
-# Final settings
 WORKDIR /tmp
-ARG BUILD_DATE
-ARG VCS_REF
-LABEL org.label-schema.build-date=$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"
+
+FROM base AS test
+
+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"
+
+ENV FSLDIR="/app/.pixi/envs/test"