Add worflows' directory

Former-commit-id: 36a35180

Docker/Dockerfile

@@ -141,7 +141,9 @@ RUN chown lofaruser:lofaruser /home/lofaruser/.entrypoint && \
 
 WORKDIR /home/lofaruser
 
-COPY scripts/* /opt/lofar/scripts/
+COPY prefactor/scripts/* /opt/lofar/scripts/
+COPY prefactor/skymodels /data/skymodels
+COPY prefactor/rfistrategies /data/rfistrategies
 
 RUN ln -sf /opt/lofar/scripts/* /usr/local/bin/
 

Docker/Dockerfile_ci

+FROM kernsuite/base:5 as builder
+SHELL ["/bin/bash", "-c"]
+
+RUN export DEBIAN_FRONTEND=noninteractive && \ 
+    apt-get update && \
+    apt-get install -y \
+        casacore-data \
+        casacore-dev \
+        libboost-python-dev \
+        libcfitsio-dev \
+        python-dev \
+        python3-numpy \
+        cmake \
+        build-essential \
+        libhdf5-serial-dev \
+        libarmadillo-dev \
+        libboost-filesystem-dev \
+        libboost-system-dev \
+        libboost-date-time-dev \
+        libboost-signals-dev \ 
+        libboost-program-options-dev \
+        libboost-test-dev \
+        libxml2-dev \
+        libpng-dev \
+        pkg-config \
+        aoflagger-dev \
+        libgtkmm-3.0-dev \
+        git \
+        wget \
+        libfftw3-dev \
+        libgsl-dev
+        
+RUN mkdir -p /src/
+WORKDIR /src/
+
+
+# Build the IDG version from source
+
+
+ADD ./idg /src/idg/src
+RUN mkdir idg/build && cd idg/build && cmake -DCMAKE_INSTALL_PREFIX=/usr/local/ ../src && make install -j2
+
+ADD ./DP3 /src/dp3/src
+RUN cd /src/dp3/  && \
+    mkdir build && \
+    cd build && \
+    cmake ../src -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=True &&\
+    make -j2 && \
+    make install -j2
+
+ADD ./STMAN /src/STMAN/src
+RUN cd /src/STMAN/ && \
+    mkdir build && \
+    cd build && \
+    cmake ../src -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=True && \
+    make -j2 && \
+    make install -j2
+    
+ADD ./Dysco /src/Dysco/src
+RUN cd /src/Dysco/ && \
+    mkdir build && \
+    cd build && \
+    cmake ../src -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=True && \
+    make -j2 && \
+    make install -j2
+
+#----------------------------------------------
+FROM kernsuite/base:4 as runner
+
+COPY --from=builder /usr/local/ /usr/local
+
+SHELL ["/bin/bash", "-c"]
+
+RUN export DEBIAN_FRONTEND=noninteractive && \
+    apt-get update && \
+    apt-get install -y \
+        aoflagger \
+        casacore-data \
+        casacore-dev \
+        libarmadillo8 \
+        libboost-date-time1.65.1 \
+        libboost-filesystem1.65.1 \
+        libboost-python1.65.1 \
+        libboost-program-options1.65.1 \
+        libboost-system1.65.1 \
+        libboost-signals1.65.1 \
+        libboost-test1.65.1 \
+        libboost-python1.65-dev \ 
+        libcfitsio5 \ 
+        libgtkmm-3.0 \
+        libfftw3-3 \
+        libhdf5-cpp-100 \
+        libpng16-16 \
+        libstationresponse0 \ 
+        libxml2 \
+        python3.7 \
+        python3-numpy \
+        python3-scipy && \
+    rm -rf /var/lib/apt/lists/*
+
+
+RUN mkdir /home/lofaruser/ && \ 
+    groupadd -r lofaruser && \
+    useradd --no-log-init -r -g lofaruser lofaruser && \
+    chown lofaruser:lofaruser /home/lofaruser
+
+ARG TOIL_VERSION=3.20.0
+LABEL toil.version=${TOIL_VERSION}
+
+ARG LSMTool_TAG=master
+LABEL LSMTool.version.tag=${LSMTool_TAG}
+
+ARG LoSoTo_TAG=master
+LABEL LoSoTo.version.tag=${LoSoTo_TAG}
+
+ARG STMAN_TAG=master
+LABEL STMAN.version.tag=${STMAN_TAG}
+
+ARG Dysco_TAG=master
+LABEL Dysco.version.tag=${Dysco_TAG}
+
+    
+RUN apt update && apt install -y nodejs python3-pip git wsclean libcasa-python3-2 wcslib-dev libcfitsio-dev
+RUN python3 -m pip install cwltool cwl-runner -e "git://github.com/darafferty/LSMTool.git@${LSMTool_TAG}#egg=LSMTool" \
+                                   "toil[cwl]"==${TOIL_VERSION} \
+                                   matplotlib \ 
+                                   python-casacore
+
+RUN python3 -m pip install -e "git+https://github.com/revoltek/losoto.git@${LoSoTo_TAG}#egg=LoSoTo"
+
+ADD L570745_uv_first10.MS.tar.xz /data
+ADD skymodels.tar.gz /data/skymodels
+ADD test_data/A-Team_lowres.sourcedb /data/A-Team_lowres.sourcedb
+ADD test_data/example.h5 /data/example.h5
+ADD test_data/L570745_SB001_uv_MODEL.MS /data/L570745_SB001_uv_MODEL.MS
+ADD losoto.patch /home/lofaruser/losoto.patch
+RUN patch /src/losoto/losoto/operations/__init__.py /home/lofaruser/losoto.patch 
+ADD .entrypoint /home/lofaruser/.entrypoint
+RUN chown lofaruser:lofaruser /home/lofaruser/.entrypoint && \ 
+    chmod +rx /home/lofaruser/.entrypoint
+
+WORKDIR /home/lofaruser
+
+COPY scripts/* /opt/lofar/scripts/
+
+RUN ln -sf /opt/lofar/scripts/* /usr/local/bin/
+
+RUN chmod +rx /usr/local/bin/*
+ENV PYTHONPATH="/opt/lofar/scripts:${PYTHONPATH}"
+ENTRYPOINT ["/home/lofaruser/.entrypoint"]
+USER lofaruser
+
+ARG DP3_TAG=master
+ARG IDG_TAG=master
+
+LABEL IDG.version.tag=${IDG_TAG}
+LABEL DP3.version.tag=${DP3_TAG}