Docker image

.github/workflows/deploy-image.yml

@@ -0,0 +1,41 @@
+name: Create and publish a Docker image
+
+on:
+  push:
+    branches: ['master']
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -0,0 +1,57 @@
+FROM continuumio/miniconda3
+
+LABEL Description="ShapePipe Docker Image"
+ENV SHELL /bin/bash
+
+ARG CC=gcc-9
+ARG CXX=g++-9
+
+# gcc < 10 is required to compile ww
+ENV CC=gcc-9
+ENV CXX=g++-9
+
+RUN apt-get update --allow-releaseinfo-change && \
+    apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install apt-utils -y && \
+    apt-get install make -y && \
+    apt-get install automake -y && \
+    apt-get install autoconf -y && \
+    apt-get install gcc-9 g++-9 -y && \
+    apt-get install locales -y && \
+    apt-get install libgl1-mesa-glx -y && \
+    apt-get install xterm -y && \
+    apt-get install cmake protobuf-compiler -y && \
+    apt-get install libtool libtool-bin libtool-doc -y && \
+    apt-get install libfftw3-bin libfftw3-dev -y && \
+    apt-get install libatlas-base-dev liblapack-dev libblas-dev -y && \
+    apt-get install vim -y && \
+    apt-get install locate -y && \
+    apt-get install curl -y && \
+    apt-get install acl -y && \
+    apt-get install sssd -y && \
+    apt-get clean
+
+ADD nsswitch.conf /etc/
+
+RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && \
+    locale-gen
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8
+
+SHELL ["/bin/bash", "--login", "-c"]
+
+COPY ./environment.yml ./
+COPY install_shapepipe README.rst setup.py setup.cfg ./
+RUN touch ./README.md
+
+RUN conda update -n base -c defaults conda -c defaults
+RUN conda env create --file environment.yml
+
+COPY shapepipe ./shapepipe
+COPY scripts ./scripts
+
+# Make RUN commands use the new environment:
+SHELL ["conda", "run", "-n", "shapepipe", "/bin/bash", "-c"]
+RUN pip install jupyter

environment.yml

@@ -4,30 +4,29 @@ channels:
 dependencies:
   - python=3.9
   - pip>=21.2.4
+  - astromatic-psfex==3.21.1
+  - astromatic-source-extractor==2.25.0
+  - astropy==5.1
+  - automake
+  - autoconf
+  - cmake
+  - galsim
+  - joblib
+  - libtool
+  - matplotlib
+  - numba
   - numpy==1.21.6
-  - astropy==5.0
-  - automake==1.16.2
-  - autoconf==2.69
-  - cmake==3.19.6
-  - galsim==2.2.5
-  - joblib==1.1.0
-  - libtool==2.4.6
-  - matplotlib==3.5.1
-  - numba==0.54.1
-  - pandas==1.4.1
   - pip:
-    - cs_util==0.0.5
-    - mccd==1.2.3
-    - modopt==1.6.0
-    - PyQt5==5.15.6
-    - pyqtgraph==0.12.4
-    - python-pysap==0.0.6
-    - reproject==0.8
-    - sip_tpv==1.1
-    - sf_tools==2.0.4
-    - sqlitedict==2.0.0
-    - termcolor==1.1.0
-    - tqdm==4.63.0
-    - treecorr==4.2.6
+    - cs_util
+    - modopt
+    - PyQt5
+    - pyqtgraph
+    - reproject
+    - sip_tpv
+    - sf_tools
+    - sqlitedict
+    - termcolor
+    - tqdm
+    - treecorr
     - git+https://github.com/aguinot/ngmix@stable_version
     - git+https://github.com/tobias-liaudat/[email protected]

example/cfis/config_exp_SpMh.ini

@@ -63,7 +63,7 @@ FILE_EXT = .fitsfz, .fitsfz, .fitsfz
 NUMBERING_SCHEME = -0000000
 
 # OUTPUT_SUFFIX, actually file name prefixes.
-# Expected keyword "flag" will lead to a behavior where the data are save as int.
+# Expected keyword "flag" will lead to a behavior where the data are saved as int.
 # The code also expects the image data to use the "image" suffix
 # (default value in the pipeline).
 OUTPUT_SUFFIX = image, weight, flag

install_shapepipe

@@ -25,20 +25,6 @@ libpng_ver="1.6.37"
 mpi4py_ver="3.1.3"
 openblas_ver="0.3.18"
 
-# SExtractor Package
-sex_url="https://github.com/astromatic/sextractor/archive/2.25.0.tar.gz"
-sex_tar="2.25.0.tar.gz"
-sex_dir="sextractor-2.25.0"
-sex_bin="sex"
-sex_version=TRUE
-
-# PSFEx Package
-psfex_url="https://github.com/astromatic/psfex/archive/3.21.1.tar.gz"
-psfex_tar="3.21.1.tar.gz"
-psfex_dir="psfex-3.21.1"
-psfex_bin="psfex"
-psfex_version=TRUE
-
 # WeightWatcher Package
 ww_url="http://snapshot.debian.org/archive/debian/20171211T160522Z/pool/main/w/weightwatcher/weightwatcher_1.12.orig.tar.gz"
 ww_tar="weightwatcher_1.12.orig.tar.gz"
@@ -84,8 +70,6 @@ ENV_NAME='shapepipe'
 BUILD_ENV=TRUE
 DEVELOP=FALSE
 VOS=FALSE
-INSTALL_SEX=TRUE
-INSTALL_PSFEX=TRUE
 INSTALL_WW=TRUE
 INSTALL_CDSCLIENT=TRUE
 ATLAS_SEARCH=FALSE
@@ -105,66 +89,6 @@ download_package() {
   rm $2
 }
 
-# Function to build SExtractor with OpenBLAS
-build_sex_blas() {
-  astromatic_setup
-  cd $BUILD_DIR/$1
-  ./autogen.sh
-  ./configure --prefix=$CONDA_PREFIX --enable-openblas --with-fftw-libdir=$FFTW_LIB \
-  --with-fftw-incdir=$FFTW_INC --with-openblas-libdir=$BLAS_LIB \
-  --with-openblas-incdir=$BLAS_INC --quiet
-  make -j --quiet
-  make install
-}
-
-# Function to build SExtractor with ATLAS
-build_sex_atlas() {
-  astromatic_setup
-  cd $BUILD_DIR/$1
-  ./autogen.sh
-  if [ "$ATLAS_SEARCH" == TRUE ]
-  then
-    ./configure --prefix=$CONDA_PREFIX --with-fftw-libdir=$FFTW_LIB \
-    --with-fftw-incdir=$FFTW_INC --quiet
-  else
-    ./configure --prefix=$CONDA_PREFIX --with-fftw-libdir=$FFTW_LIB \
-    --with-fftw-incdir=$FFTW_INC --with-atlas-libdir=$ATLAS_LIB \
-    --with-atlas-incdir=$ATLAS_INC --quiet
-  fi
-  make -j --quiet
-  make install
-}
-
-# Function to build PSFEx with OpenBLAS
-build_psfex_blas() {
-  astromatic_setup
-  cd $BUILD_DIR/$1
-  ./autogen.sh
-  ./configure --prefix=$CONDA_PREFIX --enable-openblas --enable-plplot=no \
-  --with-fftw-libdir=$FFTW_LIB --with-fftw-incdir=$FFTW_INC \
-  --with-openblas-libdir=$BLAS_LIB --with-openblas-incdir=$BLAS_INC --quiet
-  make -j --quiet
-  make install
-}
-
-# Function to build PSFEx with ATLAS
-build_psfex_atlas() {
-  astromatic_setup
-  cd $BUILD_DIR/$1
-  ./autogen.sh
-  if [ "$ATLAS_SEARCH" == TRUE ]
-  then
-    ./configure --prefix=$CONDA_PREFIX --enable-plplot=no \
-    --with-fftw-libdir=$FFTW_LIB --with-fftw-incdir=$FFTW_INC --quiet
-  else
-    ./configure --prefix=$CONDA_PREFIX --enable-plplot=no \
-    --with-fftw-libdir=$FFTW_LIB --with-fftw-incdir=$FFTW_INC \
-    --with-atlas-libdir=$ATLAS_LIB --with-atlas-incdir=$ATLAS_INC --quiet
-  fi
-  make -j --quiet
-  make install
-}
-
 # Function to build a standard package
 build_standard() {
   cd $BUILD_DIR/$1
@@ -290,8 +214,6 @@ start() {
 
 # Function to report package versions
 packages() {
-  check_binary2 $sex_bin "SExtractor" $sex_version $INSTALL_SEX
-  check_binary2 $psfex_bin "PSFEx" $psfex_version $INSTALL_PSFEX
   check_binary2 $ww_bin "WeightWatcher" $ww_version $INSTALL_WW
   check_binary2 $cdsclient_bin "CDSclient" $cdsclient_version $INSTALL_CDSCLIENT
   check_binary2 $mpi_bin "MPI" $mpi_version $USE_MPI $MPI_ROOT
@@ -332,8 +254,6 @@ package_report() {
   then
     activate_shapepipe
   fi
-  INSTALL_SEX=FALSE
-  INSTALL_PSFEX=FALSE
   INSTALL_WW=FALSE
   INSTALL_CDSCLIENT=FALSE
   USE_MPI=FALSE
@@ -381,8 +301,6 @@ setup() {
   check_status 'Operating System:' $SYSOS
   check_status 'Conda Version:' $CONDA_VERSION
   check_status 'Build Conda Environment:' $BUILD_ENV $ENV_NAME
-  check_status 'Install SExtractor:' $INSTALL_SEX
-  check_status 'Install PSFEx:' $INSTALL_PSFEX
   check_status 'Install WeightWatcher:' $INSTALL_WW
   check_status 'Install CDSclient:' $INSTALL_CDSCLIENT
   check_status 'Use MPI:' $USE_MPI $MPI_ROOT
@@ -467,8 +385,6 @@ Options:\n
 \t--develop\t option to install additional development packages\n
 \t--vos\t\t option to install virtual observatory software\n
 \t--no-env\t do not build Conda environment\n
-\t--no-sex\t do not build SExtractor\n
-\t--no-psfex\t do not build PSFEx\n
 \t--no-ww\t\t do not build WeightWatcher\n
 \t--no-cds\t do not build CDSclient\n
 \t--no-exe\t do not build any system executables\n\n
@@ -537,14 +453,6 @@ case $i in
     BUILD_ENV=FALSE
     shift
     ;;
-    --no-sex)
-    INSTALL_SEX=FALSE
-    shift
-    ;;
-    --no-psfex)
-    INSTALL_PSFEX=FALSE
-    shift
-    ;;
     --no-ww)
     INSTALL_WW=FALSE
     shift
@@ -590,8 +498,6 @@ case $i in
     shift
     ;;
     --no-exe)
-    INSTALL_SEX=FALSE
-    INSTALL_PSFEX=FALSE
     INSTALL_WW=FALSE
     INSTALL_CDSCLIENT=FALSE
     shift
@@ -716,37 +622,6 @@ fi
 # BUILD EXTERNAL EXECUTABLES
 ##############################################################################
 
-# Build SExtractor
-if [ "$INSTALL_SEX" == TRUE ] && check_binary $sex_bin
-then
-  report_progress 'SExtractor'
-  conda install -n $ENV_NAME -c conda-forge "fftw==${fftw_ver}" -y
-  download_package $sex_url $sex_tar
-  if [ "$use_atlas" == TRUE ]
-  then
-    build_sex_atlas $sex_dir
-  else
-    conda install -n $ENV_NAME -c conda-forge "openblas==${openblas_ver}" -y
-    build_sex_blas $sex_dir
-  fi
-fi
-
-# Build PSFEx
-if [ "$INSTALL_PSFEX" == TRUE ] && check_binary $psfex_bin
-then
-  report_progress 'PSFEx'
-  conda install "libpng==${libpng_ver}" -y
-  conda install -n $ENV_NAME -c conda-forge "fftw==${fftw_ver}" -y
-  download_package $psfex_url $psfex_tar
-  if [ "$use_atlas" == TRUE ]
-  then
-    build_psfex_atlas $psfex_dir
-  else
-    conda install -n $ENV_NAME -c conda-forge "openblas==${openblas_ver}" -y
-    build_psfex_blas $psfex_dir
-  fi
-fi
-
 # Build WeightWatcher
 if [ "$INSTALL_WW" == TRUE ] && check_binary $ww_bin
 then