Merge branch 'martinkilbinger-v2.0' into develop

Author: martinkilbinger

.github/workflows/deploy-image.yml

@@ -1,22 +1,19 @@
 name: Create and publish a Docker image
-
 on: [push, workflow_dispatch]
-
 env:
   REGISTRY: ghcr.io
   IMAGE_NAME: ${{ github.repository }}
   BRANCH: ${{ github.ref }}
-
 jobs:
   build-and-push-image:
-    runs-on: 
-      - ubuntu-latest
-      # - macos-latest
+    runs-on: ubuntu-latest
     permissions:
       contents: read
       packages: write
-
     steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
       - name: Log in to the Container registry
         uses: docker/login-action@v3
         with:
@@ -26,6 +23,8 @@ jobs:
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
+        with:
+          driver-opts: network=host
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
@@ -42,10 +41,10 @@ jobs:
 
       - name: Test
         run: docker run --rm ${{ steps.meta.outputs.tags }} shapepipe_run -c /app/example/config.ini
-      
+
       - name: Push
         uses: docker/build-push-action@v6
         with:
           push: true
           tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -1,100 +1,53 @@
-FROM python:3.12-slim-bookworm
+FROM images.canfar.net/skaha/astroml:latest
 
-LABEL Description="Conda-Free ShapePipe Docker Image"
-ENV SHELL=/bin/bash
-ENV QT_QPA_PLATFORM=offscreen
+# Metadata
+LABEL maintainer="martin.kilbinger@cea.fr"
+LABEL description="ShapePipe base image with common dependencies"
 
-# Install system dependencies
-RUN apt-get update -y --quiet --fix-missing && \
-    apt-get dist-upgrade -y --quiet --fix-missing && \
-    apt-cache policy autconf && \ 
-    apt-get install -y --quiet \
-    apt-utils \
-    autoconf \
-    automake \
-    build-essential \
-    cmake \
-    curl \
-    wget \
-    ffmpeg \
-    g++ \
-    gcc  \
-    gfortran \
-    git-lfs \
-    libatlas-base-dev \
-    libblas-dev \
-    liblapack-dev \
-    libcfitsio-dev \
-    libfftw3-bin \
-    libfftw3-dev \
-    libgl1-mesa-glx \
-    libgsl-dev \
-    libtool \
-    libtool-bin \
-    libtool-doc \
-    locales \
-    locate \
-    make \
-    openmpi-bin \
-    libopenmpi-dev \
-    libproj-dev \
-    proj-bin \
-    pkg-config \
-    protobuf-compiler \
-    psfex=3.21.1-1 \
-    source-extractor=2.25.0+ds-3 \
-    weightwatcher=1.12+dfsg-3 \
-    vim \
-    xterm && \
-    apt-get clean -y && \
-    apt-get autoremove --purge --quiet -y && \
-    rm -rf /var/lib/apt/lists/* /var/tmp/*
+# Install system dependencies needed for ShapePipe and WeightWatcher
+RUN apt-get update -o Acquire::ForceIPv4=true -y --quiet && \
+    apt-get install -y --no-install-recommends \
+    psfex source-extractor \
+    libproj-dev proj-bin && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
-# Install CDS client by hand
+# Build and install WeightWatcher from source
+ARG WW_VERSION=1.12
 RUN cd /tmp && \
-    curl -O http://cdsarc.u-strasbg.fr/ftp/pub/sw/cdsclient.tar.gz && \
-    tar xvfz cdsclient.tar.gz \ 
-    && cd cdsclient-* \
-    && ./configure && make && make install \
-    && rm -rf /tmp/*
+    wget --no-check-certificate https://github.com/astromatic/weightwatcher/archive/refs/tags/${WW_VERSION}.tar.gz && \
+    tar -xzf ${WW_VERSION}.tar.gz && \
+    rm ${WW_VERSION}.tar.gz
+RUN cd /tmp/weightwatcher-${WW_VERSION} && \
+    sed -i 's/^  prefstruct\tprefs;/extern prefstruct\tprefs;/' src/prefs.h && \
+    sed -i 's/^char\t\tgstr\[MAXCHAR\];/extern char\t\tgstr[MAXCHAR];/' src/globals.h && \
+    sed -i 's/^int\t\tbswapflag;/extern int\t\tbswapflag;/' src/fits/fitscat.h && \
+    sed -i '/preflist\.h/a prefstruct\tprefs;' src/prefs.c && \
+    sed -i '/xml\.h/a char\t\tgstr[MAXCHAR];' src/main.c && \
+    sed -i '/fitscat\.h/a int\t\tbswapflag;' src/fits/fitscat.c && \
+    ./configure --quiet && \
+    make --quiet && \
+    make install
 
-# Install python dependencies
+# Ensure astroml:latest conda Python 3.12 is used (Docker RUN does not source conda init)
+ENV PATH /opt/conda/bin:$PATH
+
+# Upgrade pip and install tools not part of the ShapePipe package
 RUN pip install --no-cache-dir --upgrade pip && \
     pip install --no-cache-dir \
-    astropy==6.1.0 \
-    cs_util==0.1.9 \
-    galsim==2.5.3 \
-    ipython==8.18.1 \
-    joblib==1.4.2 \
-    jupyterlab==4.3.1 \
-    matplotlib==3.8.4 \
-    mccd==1.2.4 \
-    modopt==1.6.1 \
-    mpi4py==4.0.3 \
-    numpy==1.26.4 \
-    numpydoc==1.2  \
-    pandas==2.2  \
-    pytest==8.3.3 \
-    pytest-cov==5.0.0 \
-    pytest-pycodestyle==2.4.1 \
-    pytest-pydocstyle==2.4.0 \
-    reproject==0.14.1 \
-    sf_tools==2.0.4 \
-    skaha==1.7.0 \
-    sqlitedict==2.0.0 \
-    termcolor==1.1.0 \
-    tqdm==4.63.0 \
-    vos==3.6.1.1 \
-    git+https://github.com/aguinot/ngmix@stable_version
+        ipython==8.18.1 \
+        jupyterlab==4.3.1 \
+        snakemake==8.27.1
 
+# Set working directory and copy source code
 WORKDIR /app
 COPY . /app/.
+RUN chown -R root:root /app && chmod -R u+rwX /app
 
-# Install shapepipe and symlink scripts
-RUN pip install --no-cache-dir -e . && \ 
+# Install ShapePipe and its dependencies (including fitsio optional extra)
+RUN pip install --no-cache-dir -e ".[fitsio]" && \
     for ext in .py .sh .bash; do \
-    for script in /app/scripts/*/*$ext; do \
-    link_name=`basename $script $ext`; \
-    ln -s $script /usr/local/bin/$link_name; \
-    done; \
+        for script in /app/scripts/*/*$ext; do \
+            link_name=$(basename $script $ext); \
+            ln -s $script /usr/local/bin/$link_name; \
+        done; \
     done

Dockerfile.jupyter

@@ -0,0 +1,7 @@
+# Dockerfile for ShapePipe Jupyter Lab
+# Uses the shared base image
+
+FROM ghcr.io/cosmostat/shapepipe:v2.0
+
+# Default command starts Jupyter Lab
+ENTRYPOINT ["jupyter","lab","--ip=0.0.0.0","--port=8888","--no-browser","--allow-root"]