Feature/rtofs in situ (#1138)

Created 2 converters with corresponding tests, for temperature and
salinity.
2 different files are created.
For temperature the file includes
tmp, tmp_err, lon, lat, depth
and metadata sal_typ and flg
Similarly, for salinity..

.github/workflows/norms.yaml

@@ -25,4 +25,4 @@ jobs:
     - name: Run C++ linter on utils 
       run: |
         cd $GITHUB_WORKSPACE/GDASApp/utils/test/
-        ./cpplint.py --quiet --recursive $GITHUB_WORKSPACE/GDASApp/utils
+        ./cpplint.py --quiet --recursive --exclude=$GITHUB_WORKSPACE/GDASApp/utils/obsproc/rtofs/*.cc $GITHUB_WORKSPACE/GDASApp/utils

CMakeLists.txt

@@ -8,6 +8,8 @@ cmake_minimum_required( VERSION 3.20 FATAL_ERROR )
 find_package(ecbuild 3.5 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../ecbuild)
 
 project(GDASApp VERSION 1.0.0 LANGUAGES C CXX Fortran )
+# include_directories(${CMAKE_SOURCE_DIR})
+include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 
 include(GNUInstallDirs)
 enable_testing()

utils/obsproc/CMakeLists.txt

@@ -1,2 +1,2 @@
-# add_subdirectory(rtofs)
+add_subdirectory(rtofs)
 add_subdirectory(applications)

utils/obsproc/NetCDFToIodaConverter.h

@@ -49,6 +49,9 @@ namespace gdasapp {
       oops::Log::trace() << "NetCDFToIodaConverter::NetCDFToIodaConverter created." << std::endl;
     }
 
+
+
+
     // Method to write out a IODA file (writter called in destructor)
     void writeToIoda() {
       // Extract ioda variables from the provider's files
@@ -60,6 +63,8 @@ namespace gdasapp {
 
       // Read the provider's netcdf file
       gdasapp::obsproc::iodavars::IodaVars iodaVars = providerToIodaVars(inputFilenames_[myrank]);
+
+
       for (int i = myrank + comm_.size(); i < inputFilenames_.size(); i += comm_.size()) {
         iodaVars.append(providerToIodaVars(inputFilenames_[i]));
         oops::Log::info() << " appending: " << inputFilenames_[i] << std::endl;
@@ -200,6 +205,9 @@ namespace gdasapp {
       }
     }
 
+
+
+
    private:
     // Virtual method that reads the provider's netcdf file and store the relevant
     // info in a IodaVars struct