v1.4 canfar run

.github/workflows/cd.yml

@@ -8,37 +8,45 @@ on:
 
 jobs:
 
-  api:
-    name: Deploy API Documentation
-    runs-on: ubuntu-latest
+  test-full:
+    name: Full Test Suite
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.8]
 
     steps:
       - uses: actions/checkout@v2
 
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: sudo apt-get install libopenblas-dev
+
+      - name: Install macOS Dependencies
+        shell: bash -l {0}
+        if: runner.os == 'macOS'
+        run: |
+          brew tap sfarrens/sf
+          brew install bigmac libomp
+
       - name: Set up conda
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: 3.9
+          python-version: ${{ matrix.python-version }}
           auto-activate-base: true
 
-      - name: Install dependencies
+      - name: Install package
         shell: bash -l {0}
         run: |
-          ./install_shapepipe --develop --no-exe --no-mpi
-          conda activate shapepipe
-          python -m pip install --upgrade importlib-metadata
-          conda install -c conda-forge pandoc
+          ./install_shapepipe --env-dev --develop
 
-      - name: Build API documentation
+      - name: Run tests
         shell: bash -l {0}
         run: |
-          conda activate shapepipe
-          sphinx-apidoc -t docs/_templates -feTMo docs/source shapepipe shapepipe/modules/*_runner.py
-          sphinx-build -E docs/source docs/_build
-
-      - name: Deploy API documentation
-        uses: peaceiris/actions-gh-pages@v3.5.9
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: docs/_build
+          conda activate shapepipe-dev
+          python setup.py test
+          shapepipe_run -c example/config.ini

.github/workflows/ci-dev.yml

@@ -0,0 +1,51 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+     - develop
+
+jobs:
+
+  test-full:
+    name: Full Test Suite
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.8]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: sudo apt-get install libopenblas-dev
+
+      - name: Install macOS Dependencies
+        shell: bash -l {0}
+        if: runner.os == 'macOS'
+        run: |
+          brew tap sfarrens/sf
+          brew install bigmac libomp
+
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: true
+
+      - name: Install package
+        shell: bash -l {0}
+        run: |
+          ./install_shapepipe --env-dev --develop
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          conda activate shapepipe-dev
+          python setup.py test
+          shapepipe_run -c example/config.ini

.github/workflows/ci-tests.yml → .github/workflows/ci-release.yml

@@ -5,7 +5,6 @@ on:
     branches:
      - main
      - master
-     - develop
 
 jobs:
 

.github/workflows/deploy-image.bak.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 }}

.github/workflows/deploy-image.yml

@@ -0,0 +1,38 @@
+name: Create and publish a Docker image
+
+on:
+  push:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: 
+      - ubuntu-latest
+      # - macos-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.gitignore

@@ -133,3 +133,4 @@ dmypy.json
 # Ignore example output
 *shapepipe_run_*
 *shapepipe_runs*
+code

Dockerfile

@@ -0,0 +1,103 @@
+FROM python:3.9-bookworm
+
+LABEL Description="Conda-Free ShapePipe Docker Image"
+ENV SHELL=/bin/bash
+
+# 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 \
+    ffmpeg \
+    g++ \
+    gcc  \
+    gfortran \
+    git-lfs \
+    libatlas-base-dev \
+    libblas-dev \
+    liblapack-dev \
+    libcfitsio-dev \
+    libfftw3-bin \
+    libfftw3-dev \
+    libgl1-mesa-glx \
+    libtool \
+    libtool-bin \
+    libtool-doc \
+    locales \
+    locate \
+    make \
+    openmpi-bin \
+    libopenmpi-dev \
+    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 CDS client by hand
+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/*
+
+# Install python dependencies
+RUN pip install --no-cache-dir --upgrade pip && \
+    pip install --no-cache-dir \
+    astropy==5.2 \
+    cs_util==0.1.0 \
+    galsim==2.2.6 \
+    ipython==8.18.1 \
+    joblib==1.1.0 \
+    jupyterlab==4.3.1 \
+    matplotlib==3.8.4 \
+    mccd==1.2.4 \
+    modopt==1.6.1 \
+    mpi4py==3.1.3 \
+    numba==0.58.1 \
+    numpy==1.26.4 \
+    numpydoc==1.2  \
+    pandas==1.4.1  \
+    PyQt5==5.15.6 \
+    pyqtgraph==0.12.4 \
+    pytest==8.3.3 \
+    pytest-cov==5.0.0 \
+    pytest-pycodestyle==2.4.1 \
+    pytest-pydocstyle==2.4.0 \
+    python-pysap==0.2.1 \
+    reproject==0.8 \
+    sf_tools==2.0.4 \
+    sip_tpv==1.1 \
+    skaha==1.4.3 \
+    sqlitedict==2.0.0 \
+    termcolor==1.1.0 \
+    tqdm==4.63.0 \
+    treecorr==4.2.6 \
+    vos==3.6.1.1 \
+    git+https://github.com/aguinot/ngmix@stable_version \
+    git+https://github.com/tobias-liaudat/Stile@v0.1
+
+
+WORKDIR /app
+COPY . /app/.
+
+# Install shapepipe and symlink scripts
+RUN pip install --no-cache-dir -e . && \ 
+    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; \
+    done