Merge remote-tracking branch 'origin/v1.4' into wcs_mk

.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.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 gfortran -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
+
+RUN source activate shapepipe
+#RUN pip install jupyter

auxdir/CFIS/tiles_202402/tiles_COSMOS.txt

@@ -0,0 +1,9 @@
+299.183
+300.183
+301.183
+299.184
+300.184
+301.184
+299.185
+300.185
+301.185