Introduce the bufr_query library from NOAA-EMC (spack#45920)

* Introduce the bufr_query library from NOAA-EMC (spack#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.

* Add explicit build dependency spec to the pybind11 depends_on spec

Co-authored-by: Wouter Deconinck <[email protected]>

* Convert patch file to the URL form which pulls the changes from github.

Co-authored-by: Wouter Deconinck <[email protected]>

* Added new version (0.0.3) and removed obsolete site-packages.patch file

---------

Co-authored-by: Wouter Deconinck <[email protected]>

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

@@ -0,0 +1,59 @@
+# 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("0.0.3", sha256="f2952a190cc1d7714a3bfe481fb1545459639ba304fc31b941062b471dea1d41")
+    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", type="build")
+
+    # Patches
+    patch(
+        "https://github.com/NOAA-EMC/bufr-query/pull/20.patch?full_index=1",
+        sha256="3acf11082c9e76e64dbbda4f62ac0cbc234dca7e60c85a275e778417cfd65001",
+        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