MNT: Define conda environment, refactor Dockerfile

Dockerfile

@@ -22,26 +22,140 @@
 # 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-20230308
+
+#
+# Build wheel
+#
 FROM python:slim AS src
 RUN pip install build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends git
-COPY . /src/niworkflows
-RUN python -m build /src/niworkflows
+COPY . /src
+RUN python -m build /src
 
-FROM nipreps/miniconda:py39_2209.01
+#
+# Download stages
+#
 
-ARG DEBIAN_FRONTEND=noninteractive
-ENV LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${CONDA_PATH}/lib"
+# Utilities for downloading packages
+FROM ${BASE_IMAGE} as downloader
+# Bump the date to current to refresh curl/certificates/etc
+RUN echo "2023.12.12"
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    binutils \
+                    bzip2 \
+                    ca-certificates \
+                    curl \
+                    unzip && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# 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 "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 \( \
+        -name "3dTshift" -or \
+        -name "3dUnifize" -or \
+        -name "3dAutomask" -or \
+        -name "3dvolreg" \) -delete
 
-# Installing freesurfer
-COPY docker/files/freesurfer7.2-exclude.txt /usr/local/etc/freesurfer7.2-exclude.txt
-RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz \
-    | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.2-exclude.txt
+# Micromamba
+FROM downloader as micromamba
+WORKDIR /
+# Bump the date to current to force update micromamba
+RUN echo "2023.04.05"
+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 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 FSL_DIR="/opt/fsl" \
-    OS="Linux" \
+ENV OS="Linux" \
     FS_OVERRIDE=0 \
     FIX_VERTEX_AREA="" \
     FSF_OUTPUT_FORMAT="nii.gz" \
@@ -55,120 +169,55 @@ ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
     MNI_DATAPATH="$FREESURFER_HOME/mni/data"
 ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
     MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
-    PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
-
-# Install AFNI latest (neurodocker build)
-ENV AFNI_DIR="/opt/afni"
-RUN echo "Downloading AFNI ..." \
-    && mkdir -p ${AFNI_DIR} \
-    && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
-       | tar -xz -C ${AFNI_DIR} --strip-components 1 \
-    # Keep only what we use
-    && find ${AFNI_DIR} -type f -not \( \
-        -name "3dTshift" -or \
-        -name "3dUnifize" -or \
-        -name "3dAutomask" -or \
-        -name "3dvolreg" \) -delete
+    PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
 
-ENV PATH="${AFNI_DIR}:$PATH" \
+# AFNI config
+ENV PATH="/opt/afni-latest:$PATH" \
     AFNI_IMSAVE_WARNINGS="NO" \
-    AFNI_MODELPATH="${AFNI_DIR}/models" \
-    AFNI_TTATLAS_DATASET="${AFNI_DIR}/atlases" \
-    AFNI_PLUGINPATH="${AFNI_DIR}/plugins"
-
-# Install AFNI's dependencies
-RUN ${CONDA_PATH}/bin/conda install -c conda-forge -c anaconda \
-                            gsl                                \
-                            xorg-libxp                         \
-    && sync \
-    && ${CONDA_PATH}/bin/conda clean -afy; sync \
-    && rm -rf ~/.conda ~/.cache/pip/*; sync \
-    && ln -s ${CONDA_PATH}/lib/libgsl.so.25 /usr/lib/x86_64-linux-gnu/libgsl.so.19 \
-    && ln -s ${CONDA_PATH}/lib/libgsl.so.25 /usr/lib/x86_64-linux-gnu/libgsl.so.0 \
-    && ldconfig
-
-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 focal main" > /etc/apt/sources.list.d/linuxuprising.list
-
-RUN apt-get update \
- && apt-get install -y -q --no-install-recommends     \
-                    libcurl4-openssl-dev              \
-                    libgdal-dev                       \
-                    libgfortran-8-dev                 \
-                    libgfortran4                      \
-                    libglw1-mesa                      \
-                    libgomp1                          \
-                    libjpeg62                         \
-                    libpng12-0                        \
-                    libnode-dev                       \
-                    libssl-dev                        \
-                    libudunits2-dev                   \
-                    libxm4                            \
-                    libxml2-dev                       \
-                    netpbm                            \
-                    tcsh                              \
-                    xfonts-base                       \
- && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
- && ldconfig
-
-# Installing ANTs 2.3.4 (NeuroDocker build)
-ENV ANTSPATH="/opt/ants"
-WORKDIR $ANTSPATH
-RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
-    | tar -xzC $ANTSPATH --strip-components 1
-ENV PATH="$ANTSPATH:$PATH"
-
-# FSL 6.0.5.1
-RUN curl -sSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz | tar zxv --no-same-owner -C /opt \
-    --exclude='fsl/doc' \
-    --exclude='fsl/refdoc' \
-    --exclude='fsl/python/oxford_asl' \
-    --exclude='fsl/data/possum' \
-    --exclude='fsl/data/first' \
-    --exclude='fsl/data/mist' \
-    --exclude='fsl/data/atlases' \
-    --exclude='fsl/data/xtract_data' \
-    --exclude='fsl/extras/doc' \
-    --exclude='fsl/extras/man' \
-    --exclude='fsl/extras/src' \
-    --exclude='fsl/src' \
-    --exclude='fsl/tcl'
-
-ENV FSLDIR="/opt/fsl" \
-    PATH="/opt/fsl/bin:$PATH" \
-    FSLOUTPUTTYPE="NIFTI_GZ" \
-    FSLMULTIFILEQUIT="TRUE" \
-    FSLTCLSH="/opt/fsl/bin/fsltclsh" \
-    FSLWISH="/opt/fsl/bin/fslwish" \
-    FSLLOCKDIR="" \
-    FSLMACHINELIST="" \
-    FSLREMOTECALL="" \
-    FSLGECUDAQ="cuda.q" \
-    POSSUMDIR="/opt/fsl" \
-    LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/opt/fsl"
-
-# Unless otherwise specified each process should only use one thread - nipype
-# will handle parallelization
-ENV MKL_NUM_THREADS=1 \
-    OMP_NUM_THREADS=1
+    AFNI_PLUGINPATH="/opt/afni-latest"
 
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users niworkflows
 WORKDIR /home/niworkflows
 ENV HOME="/home/niworkflows" \
     LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$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
+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
 
 # Installing niworkflows
-COPY --from=src /src/niworkflows/dist/*.whl .
-RUN /opt/conda/bin/python -m pip install --no-cache-dir $( ls *.whl )[all]
+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