Introduce the bufr_query library from NOAA-EMC (#461)

This PR adds in a new package.py script for the new bufr_query library from NOAA-EMC. This is being used by JEDI and other applications.

var/spack/repos/builtin/packages/bufr-query/package.py

@@ -0,0 +1,54 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class BufrQuery(CMakePackage, PythonExtension):
+    """The NOAA bufr-query Library can be used to read NCEP and WMO formated BUFR
+    files using a simple interface that does not require the user to know the
+    details of the BUFR format. Detailed documentation for the BUFR Library can
+    be found at https://bufr-query.readthedocs.io/en/latest/index.html"""
+
+    homepage = "https://github.com/NOAA-EMC/bufr-query"
+    url = "https://github.com/NOAA-EMC/bufr-query/archive/refs/tags/v0.0.1.tar.gz"
+    maintainers("srherbener", "rmclaren")
+
+    license("Apache-2.0", checked_by="srherbener")
+
+    version("0.0.2", sha256="b87a128246e79e3c76e3158d89823e2ae38e9ee1a5a81b6f7b423837bdb93a1f")
+    version("0.0.1", sha256="001990d864533c101b93d1c351edf50cf8b5ccc575e442d174735f6c332d3d03")
+
+    # Required dependencies
+    depends_on("ecbuild", type=("build"))
+    depends_on("llvm-openmp", when="%apple-clang", type=("build", "run"))
+    depends_on("mpi", type=("build", "run"))
+    depends_on("[email protected]:", type=("build", "run"))
+    depends_on("eigen@3:", type=("build", "run"))
+    depends_on("gsl-lite", type=("build", "run"))
+    depends_on("netcdf-c", type=("build", "run"))
+    depends_on("netcdf-cxx4", type=("build", "run"))
+    depends_on("bufr", type=("build", "run"))
+
+    # Optional dependencies
+    variant("python", default=True, description="Enable Python interface")
+
+    with when("+python"):
+        extends("python")
+        depends_on("py-pybind11")
+
+    # Patches
+    patch("site-packages.patch", when="+python @:0.0.2")
+
+    # CMake configuration
+    def cmake_args(self):
+        args = [self.define_from_variant("BUILD_PYTHON_BINDINGS", "python")]
+
+        # provide path to netcdf-c include files
+        nc_include_dir = Executable("nc-config")("--includedir", output=str).strip()
+        args.append("-DCMAKE_C_FLAGS=-I" + nc_include_dir)
+        args.append("-DCMAKE_CXX_FLAGS=-I" + nc_include_dir)
+
+        return args

var/spack/repos/builtin/packages/bufr-query/site-packages.patch

@@ -0,0 +1,93 @@
+diff --git a/cmake/Targets.cmake b/cmake/Targets.cmake
+index 42dc2bc..8a26827 100644
+--- a/cmake/Targets.cmake
++++ b/cmake/Targets.cmake
+@@ -104,17 +104,17 @@ macro(AddPyLib libname pyname pybasename)
+     ApplyBaseSettings(${libname})
+     set_target_properties( ${libname} PROPERTIES FOLDER "Libs/Python/${pybasename}")
+     set_target_properties( ${libname} PROPERTIES
+-        ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib/${pybasename}/${pyname}"
+-        LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib/${pybasename}/${pyname}"
+-        RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin/${pybasename}/${pyname}"
++        ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib/${pybasename}/site-packages/${pyname}"
++        LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib/${pybasename}/site-packages/${pyname}"
++        RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin/${pybasename}/site-packages/${pyname}"
+         INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}"
+         )
+     export( TARGETS ${libname} APPEND FILE "${PROJECT_TARGETS_FILE}" )
+     install( TARGETS ${libname}
+         EXPORT ${PROJECT_NAME}-targets
+         RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+-        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}/${pybasename}/${pyname}
+-        ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}/${pybasename}/${pyname}
++        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}/${pybasename}/site-packages/${pyname}
++        ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}/${pybasename}/site-packages/${pyname}
+         COMPONENT Python)
+ endmacro(AddPyLib)
+
+diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
+index 1082d30..cf4fd54 100644
+--- a/python/CMakeLists.txt
++++ b/python/CMakeLists.txt
+@@ -5,28 +5,21 @@ include(Targets)
+ # Location of .pycodestyle for norm checking within IODA-converters
+ set( BUFR_PYLINT_CFG_DIR ${CMAKE_CURRENT_SOURCE_DIR} )
+
+-set(pyver python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR})
+-set(PYDIR ${pyver}/bufr)
+-
+-# Location of installed python iodaconv libraries
+-set( PYIODACONV_BUILD_LIBDIR   ${CMAKE_BINARY_DIR}/lib/${PYDIR} )
+-set( PYIODACONV_INSTALL_LIBDIR ${CMAKE_INSTALL_PREFIX}/lib/${PYDIR} )
+-
+-
+-list (APPEND PYTHON_SRCS DataObjectFunctions.h
+-												DataObjectFunctions.cpp
+-												py_bufr.cpp
+-												py_result_set.cpp
+-												py_data_container.cpp
+-												py_query_set.cpp
+-												py_file.cpp
+-												py_parser.cpp
+-												py_data_cache.cpp
+-											  py_encoder_description.cpp
+-												py_netcdf_encoder.cpp
+-												py_mpi.h
+-												py_mpi.cpp
+-												)
++list (APPEND PYTHON_SRCS
++  DataObjectFunctions.h
++  DataObjectFunctions.cpp
++  py_bufr.cpp
++  py_result_set.cpp
++  py_data_container.cpp
++  py_query_set.cpp
++  py_file.cpp
++  py_parser.cpp
++  py_data_cache.cpp
++  py_encoder_description.cpp
++  py_netcdf_encoder.cpp
++  py_mpi.h
++  py_mpi.cpp
++)
+
+ # We cannot call ecbuild_add_library here since it conflicts with pybind11_add_module.
+ pybind11_add_module(bufr_python ${PYTHON_SRCS})
+@@ -51,13 +44,7 @@ else()
+ 		)
+ endif()
+
+-add_custom_command(TARGET bufr_python
+-									 POST_BUILD
+-									 COMMAND ${CMAKE_COMMAND} -E copy_directory
+-	                 				 ${CMAKE_CURRENT_SOURCE_DIR}/bufr
+-													 $<TARGET_FILE_DIR:bufr_python>)
+-
+ install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/bufr
+-	      DESTINATION ${CMAKE_INSTALL_LIBDIR}/${pyver}
+-			  COMPONENT Python
+-	      FILES_MATCHING PATTERN "*.py")
++        DESTINATION ${CMAKE_INSTALL_LIBDIR}/${pyver}/site-packages
++        COMPONENT Python
++        FILES_MATCHING PATTERN "*.py")
+