Issue 68 (#69)

* Ensure python3 is used to detect numpy for cmake build
* Fixes #68

.ci/py3.docker

@@ -0,0 +1,110 @@
+FROM kernsuite/base:7
+
+RUN docker-apt-install libblitz0-dev python3-dev libblas-dev liblapack-dev libqdbm-dev wcslib-dev \
+ libfftw3-dev python3-numpy libcfitsio-dev libboost-all-dev libboost-system-dev cmake g++ wget gfortran \
+ libncurses5-dev bison libbison-dev flex libreadline6-dev python3-pip rsync
+
+#####################################################################
+## Get CASACORE ephem data
+#####################################################################
+RUN mkdir -p /usr/share/casacore/data/
+WORKDIR /usr/share/casacore/data/
+RUN rsync -avz rsync://casa-rsync.nrao.edu/casa-data .
+
+#####################################################################
+## BUILD CASACORE AND CASAREST FROM SOURCE
+## -- Kern version is missing executables from casarest
+#####################################################################
+WORKDIR /src
+RUN wget https://github.com/casacore/casacore/archive/v3.4.0.tar.gz && \
+    tar xvf v3.4.0.tar.gz && \
+    rm v3.4.0.tar.gz && \
+    mkdir casacore-3.4.0/build && \
+    cd /src/casacore-3.4.0/build && \
+    cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DBUILD_DEPRECATED=ON -DBUILD_PYTHON=OFF -DBUILD_PYTHON3=ON ../ && \
+    make -j 4 && \
+    make install && \
+    rm -r /src/casacore-3.4.0 && \
+    cd /src && \
+    wget https://github.com/casacore/casarest/archive/v1.8.0.tar.gz && \
+    tar xvf v1.8.0.tar.gz && \
+    rm v1.8.0.tar.gz && \
+    cd /src/casarest-1.8.0 && \
+    mkdir -p build && \
+    cd /src/casarest-1.8.0/build && \
+    cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../ && \
+    make -j 4 && \
+    make install && \
+    rm -r /src/casarest-1.8.0 && \
+    ldconfig && \
+    cd /src && \
+    wget https://github.com/casacore/python-casacore/archive/v3.4.0.tar.gz && \
+    tar xvf v3.4.0.tar.gz && \
+    rm v3.4.0.tar.gz && \
+    cd /src/python-casacore-3.4.0 && \
+    python3.8 -m pip install . && \
+    cd / && \
+    python3.8 -c "from pyrap.tables import table as tbl"
+
+
+#####################################################################
+## BUILD MAKEMS FROM SOURCE AND TEST
+#####################################################################
+WORKDIR /src
+RUN wget https://github.com/ska-sa/makems/archive/v1.5.4.tar.gz && \
+    tar xvf v1.5.4.tar.gz && \
+    rm v1.5.4.tar.gz && \
+    mkdir -p /src/makems-1.5.4/LOFAR/build/gnu_opt && \
+    cd /src/makems-1.5.4/LOFAR/build/gnu_opt && \
+    cmake -DCMAKE_MODULE_PATH:PATH=/src/makems-1.5.4/LOFAR/CMake \
+          -DUSE_LOG4CPLUS=OFF -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=Release \
+          -DCMAKE_INSTALL_PREFIX=/usr ../.. && \
+    make -j 16 && \
+    make install && \
+    cd /src/makems-1.5.4/test && \
+    makems WSRT_makems.cfg && \
+    rm -r /src/makems-1.5.4
+
+#####################################################################
+## BUILD MeqTrees from source
+#####################################################################
+WORKDIR /src
+
+# Get MeqTrees universe python packages
+RUN python3.8 -m pip install purr owlcat kittens 'meqtrees-cattery>=1.7.6' astro-tigger-lsm
+
+ADD . /code
+RUN mkdir /code/build && \
+    cd /code/build && \
+    cmake -DCMAKE_INSTALL_PREFIX=/usr \
+          -DCMAKE_BUILD_TYPE=Release \
+          -DENABLE_PYTHON_3=ON \
+          .. && \
+    make -j4 && \
+    make install && \
+    rm -r /code/build && \
+    ldconfig
+
+
+#####################################################################
+## Run tests
+#####################################################################
+
+# basic install tests
+RUN flag-ms.py --help
+RUN meqtree-pipeliner.py --help
+RUN pyxis --help
+
+# run test when built
+WORKDIR /src
+RUN pip3 install nose && \
+    wget https://github.com/ska-sa/pyxis/archive/v1.7.4.3.tar.gz && \
+    tar -xvf v1.7.4.3.tar.gz && \
+    rm v1.7.4.3.tar.gz && \
+    python3.8 -m pip install /src/pyxis-1.7.4.3 && \
+    cd /src/pyxis-1.7.4.3/Pyxis/recipes/meqtrees-batch-test && \
+    python3 -m "nose" && \
+    rm -r /src/pyxis-1.7.4.3
+
+ENTRYPOINT ["meqtree-pipeliner.py"]
+CMD ["--help"]

.dockerignore

@@ -1,3 +1,4 @@
 .git
 build
 Dockerfile
+.ci

AppAgent/AppUtils/src/MSInputChannel.cc

@@ -689,9 +689,9 @@ int MSInputChannel::refillStream ()
             predcube.reverseSelf(blitz::secondDim);
         }
         // get vector of row numbers
-        Vector<uInt> rownums = table.rowNumbers(ms_);
+        auto rownums = table.rowNumbers(ms_);
     // now process rows one by one
-        for( int i=0; i<nrows; i++ )
+        for( size_t i=0; i<nrows; i++ )
         {
           int ant1 = ant1col(i), ant2 = ant2col(i);
           if( ant1 < 0 || ant1 >= num_antennas_ )

AppAgent/AppUtils/src/wsrt_j2convert.cc

@@ -26,6 +26,7 @@
 //# $Id: j2convert.cc,v 19.3 2004/11/30 17:50:39 ddebonis Exp $
 
 //# Includes
+#include <casacore/casa/version.h>
 #include <casacore/measures/Measures/Muvw.h>
 #include <casacore/measures/Measures/MCBaseline.h>
 #include <casacore/measures/Measures/MBaseline.h>
@@ -56,7 +57,11 @@
 #include <casacore/measures/TableMeasures/TableMeasRefDesc.h>
 #include <casacore/casa/Arrays/Vector.h>
 #include <casacore/casa/Arrays/ArrayMath.h>
-#include <casacore/casa/Arrays/ArrayIO.h>
+#if CASACORE_MAJOR_VERSION <= 3 && CASACORE_MINOR_VERSION < 4
+	#include <casacore/casa/Arrays/ArrayIO.h>
+#else
+	#include <casacore/casa/IO/ArrayIO.h>
+#endif
 #include <casacore/casa/Arrays/MatrixMath.h>
 #include <casacore/casa/System/ProgressMeter.h>
 #include <casacore/casa/Inputs.h>

Jenkinsfile.sh

@@ -21,4 +21,4 @@ cd $PROJECTS_DIR/meqtrees-timba
 IMAGENAME="mttimbapr"
 
 # build and test
-docker build -f .travis/py3.docker -t "${IMAGENAME}36:$BUILD_NUMBER" --no-cache=true .
+docker build -f .ci/py3.docker -t "${IMAGENAME}36:$BUILD_NUMBER" --no-cache=true .

MeqNodes/src/CasaParmTable.cc

@@ -208,7 +208,7 @@ int CasaParmTable::getFunklets (vector<Funklet::Ref> &funklets,
       if(itsTable.actualTableDesc().isColumn(ColFunkletType))
 	ftypeCol.attach(sel, ColFunkletType);    
       ROArrayColumn<double> lscaleCol;
-      Vector<uInt> rowNums = sel.rowNumbers(itsTable);
+      auto rowNums = sel.rowNumbers(itsTable);
       int axis[] = { Axis::TIME,Axis::FREQ };
       for( uint i=0; i<sel.nrow(); i++ )
 	{
@@ -272,7 +272,7 @@ int CasaParmTable::getInitCoeff (Funklet::Ref &funkletref,const string& parmName
     while( true ) 
     {
       *itsInitIndexName   = name;
-      Vector<uInt> rownrs = itsInitIndex->getRowNumbers();
+      auto rownrs = itsInitIndex->getRowNumbers();
       if (rownrs.nelements() > 0) 
       {
         Assert( rownrs.nelements() == 1 );
@@ -454,7 +454,7 @@ Table CasaParmTable::find (const string& parmName,
   // First see if the parameter name exists at all.
   Table result;
   *itsIndexName   = parmName;
-  Vector<uInt> rownrs = itsIndex.getRowNumbers();
+  auto rownrs = itsIndex.getRowNumbers();
   if (rownrs.nelements() > 0) {
     Table sel = itsTable(rownrs);
     // Find all rows overlapping the requested domain.

cmake/FindPythonNumpy.cmake

@@ -17,7 +17,7 @@ EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c "import numpy;print(numpy.get_in
   OUTPUT_STRIP_TRAILING_WHITESPACE)
 
 IF ( ${NUMPY_FIND_RESULT} )
-  MESSAGE( "python -c 'import numpy' appears to fail. Is numpy installed?" )
+  MESSAGE( "python3 -c 'import numpy' appears to fail. Is numpy installed?" )
   SET(PYTHON_NUMPY_INCLUDE_DIR) 
   FIND_PATH(PYTHON_NUMPY_INCLUDE_DIR numpy)
 ENDIF ( ${NUMPY_FIND_RESULT} )