Merge pull request #10 from nipreps-containers/enh/update-to-micromamba

ENH: Migrate to micromamba

Dockerfile

@@ -20,7 +20,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 # Use Ubuntu 20.04 LTS
-FROM ubuntu:focal-20210416
+FROM ubuntu:jammy-20240125
 
 # Make apt non-interactive
 RUN echo 'APT::Get::Assume-Yes "true";' > /etc/apt/apt.conf.d/90circleci \
@@ -35,6 +35,7 @@ RUN apt-get update && \
                     build-essential \
                     bzip2 \
                     ca-certificates \
+                    curl \
                     libtool \
                     locales \
                     lsb-release \
@@ -50,102 +51,33 @@ RUN locale-gen en_US.UTF-8 || true
 ENV LANG="en_US.UTF-8" \
     LC_ALL="en_US.UTF-8"
 
-# Leave these args here to better use the Docker build cache
-# miniconda index: https://conda.io/en/latest/miniconda_hashes.html
-ENV CONDA_PATH="/opt/conda"
-ARG CONDA_VERSION=py39_23.1.0-1
-ARG SHA256SUM=5dc619babc1d19d6688617966251a38d245cb93d69066ccde9a013e1ebb5bf18
+WORKDIR /
+RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 
-RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-${CONDA_VERSION}-Linux-x86_64.sh -O miniconda.sh && \
-    echo "${SHA256SUM}  miniconda.sh" > miniconda.sha256 && \
-    sha256sum -c --status miniconda.sha256 && \
-    mkdir -p /opt && \
-    sh miniconda.sh -b -p ${CONDA_PATH} && \
-    rm miniconda.sh miniconda.sha256 && \
-    ln -s ${CONDA_PATH}/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
-    echo ". ${CONDA_PATH}/etc/profile.d/conda.sh" >> ~/.bashrc && \
-    echo "conda activate base" >> ~/.bashrc && \
-    find ${CONDA_PATH}/ -follow -type f -name '*.a' -delete && \
-    find ${CONDA_PATH}/ -follow -type f -name '*.js.map' -delete && \
-    ${CONDA_PATH}/bin/conda clean -afy
-
-# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
-ENV PATH="${CONDA_PATH}/bin:$PATH" \
-    CPATH="${CONDA_PATH}/include:$CPATH" \
-    PYTHONNOUSERSITE=1
-
-COPY condarc /root/.condarc
-
-RUN ${CONDA_PATH}/bin/conda install mamba -n base && \
-    mamba install -y \
-        attrs=22.2 \
-        codecov=2.1 \
-        colorclass=2.2 \
-        coverage=6.3 \
-        curl=7.88 \
-        datalad=0.18 \
-        dipy=1.5 \
-        flake8=4.0 \
-        git=2.39 \
-        graphviz=3.0 \
-        h5py=3.8 \
-        indexed_gzip=1.7 \
-        jinja2=3.1 \
-        libxml2=2.10 \
-        libxslt=1.1 \
-        lockfile=0.12 \
-        matplotlib=3.5 \
-        mkl=2022.1 \
-        mkl-service=2.4 \
-        nibabel=4.0 \
-        nilearn=0.9 \
-        nipype=1.8 \
-        nitime=0.9 \
-        nodejs=18 \
-        numpy=1.24 \
-        packaging=23.0 \
-        pandas=1.5 \
-        pandoc=2.19 \
-        pbr=5.11 \
-        pip=23.0 \
-        pockets=0.9 \
-        psutil=5.9 \
-        pydot=1.4 \
-        pytest=7.2 \
-        pytest-cov=4.0 \
-        pytest-env=0.8 \
-        pytest-xdist=3.2 \
-        pyyaml=6.0 \
-        requests=2.28 \
-        scikit-image=0.19 \
-        scikit-learn=1.2 \
-        scipy=1.10 \
-        seaborn=0.12 \
-        setuptools=65 \
-        sphinx=4.5 \
-        sphinx_rtd_theme=1.0 \
-        svgutils=0.3 \
-        toml=0.10 \
-        traits=6.3 \
-        zlib=1.2 \
-        zstd=1.5; sync && \
-    chmod -R a+rX ${CONDA_PATH}; sync && \
-    chmod +x ${CONDA_PATH}/bin/*; sync && \
-    ${CONDA_PATH}/bin/conda clean -afy && sync && \
-    rm -rf ~/.conda ~/.cache/pip/*; sync
+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
 
 # Precaching fonts, set 'Agg' as default backend for matplotlib
-RUN ${CONDA_PATH}/bin/python -c "from matplotlib import font_manager" && \
-    sed -i 's/\(backend *: \).*$/\1Agg/g' $( ${CONDA_PATH}/bin/python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
+RUN micromamba -n base run python -c "from matplotlib import font_manager" && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' $( micromamba -n base run python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
 
-# Install packages that are not distributed with conda
-RUN ${CONDA_PATH}/bin/python -m pip install --no-cache-dir -U \
-                      datalad-osf \
-                      etelemetry \
-                      nitransforms \
-                      templateflow \
-                      transforms3d
+# UV_USE_IO_URING for apparent race-condition (https://github.com/nodejs/node/issues/48444)
+# Check if this is still necessary when updating the base image.
+ENV PATH="/opt/conda/bin:$PATH" \
+    UV_USE_IO_URING=0
 
 # Installing SVGO and bids-validator
-RUN ${CONDA_PATH}/bin/npm install -g svgo@^2.3 bids-validator@1.8.0 && \
+RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
     rm -rf ~/.npm ~/.empty /root/.npm
+
+# Initialize templateflow
+ENV TEMPLATEFLOW_HOME=/templateflow
+RUN templateflow update
+
+# Pacify DataLad
+RUN git config --global user.name "NiPreps Miniconda" \
+    && git config --global user.email "[email protected]"

env.yml

@@ -0,0 +1,31 @@
+name: base
+channels:
+  - conda-forge
+# Update this ~yearly; last updated Jan 2024
+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
+  - pip
+  - pip:
+    - -r requirements.txt
+variables:
+  FSLOUTPUTTYPE: NIFTI_GZ