Update bufr recipe (#40033)

* Update bufr recipe
* Add v12.0.1
* style fixes
* remove test-related functionality for bufr
* Re-add testing

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

var/spack/repos/builtin/packages/bufr/c-tests-libm.patch

@@ -0,0 +1,11 @@
+--- a/test/CMakeLists.txt	2022-07-28 11:25:13.000000000 -0400
++++ b/test/CMakeLists.txt	2022-07-28 11:26:40.000000000 -0400
+@@ -205,7 +205,7 @@
+     set(test_exe ${test}.x)
+     add_executable(${test_exe} ${test_src})
+     add_dependencies(${test_exe} bufr_${kind})
+-    target_link_libraries(${test_exe} PRIVATE bufr::bufr_${kind})
++    target_link_libraries(${test_exe} PRIVATE bufr::bufr_${kind} m)
+     add_test(NAME ${test} COMMAND ${CMAKE_BINARY_DIR}/test/${test_exe})
+   endforeach()
+ endforeach()

var/spack/repos/builtin/packages/bufr/cmakelists-apple-llvm-ranlib.patch

@@ -0,0 +1,15 @@
+--- a/CMakeLists.txt	2022-02-08 10:03:55.000000000 -0700
++++ b/CMakeLists.txt	2022-02-08 10:03:51.000000000 -0700
+@@ -39,9 +39,9 @@
+   find_package(Python3 REQUIRED COMPONENTS Interpreter)
+ endif()
+ 
+-if(APPLE)
+-  # The linker on macOS does not include `common symbols` by default
+-  # Passing the -c flag includes them and fixes an error with undefined symbols
++if(APPLE AND NOT "${CMAKE_RANLIB}" MATCHES "^.*(llvm-ranlib)$")
++  # The linker on macOS does not include `common symbols` by default, Intel requires
++  # passing the -c flag to include them and fix an error with undefined symbols
+   set(CMAKE_Fortran_ARCHIVE_FINISH "<CMAKE_RANLIB> -c <TARGET>")
+   set(CMAKE_C_ARCHIVE_FINISH "<CMAKE_RANLIB> -c <TARGET>")
+ endif()

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

@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
+
 from spack.package import *
 
 
@@ -11,37 +13,109 @@ class Bufr(CMakePackage):
     utilities that can be used to read (decode) and write (encode)
     data in BUFR, which is a WMO standard format for the exchange of
     meteorological data. This is part of the NCEPLIBS project.
-
+    The library also includes a Python interface.
     """
 
     homepage = "https://noaa-emc.github.io/NCEPLIBS-bufr"
     url = "https://github.com/NOAA-EMC/NCEPLIBS-bufr/archive/refs/tags/bufr_v11.5.0.tar.gz"
+    git = "https://github.com/NOAA-EMC/NCEPLIBS-bufr"
 
-    maintainers("t-brown", "AlexanderRichert-NOAA", "edwardhartnett", "Hang-Lei-NOAA", "jbathegit")
+    maintainers("AlexanderRichert-NOAA", "edwardhartnett", "Hang-Lei-NOAA", "jbathegit")
 
+    version("develop", branch="develop")
+    version("12.0.1", sha256="525f26238dba6511a453fc71cecc05f59e4800a603de2abbbbfb8cbb5adf5708")
+    version("12.0.0", sha256="d01c02ea8e100e51fd150ff1c4a1192ca54538474acb1b7f7a36e8aeab76ee75")
     version("11.7.1", sha256="6533ce6eaa6b02c0cb5424cfbc086ab120ccebac3894980a4daafd4dfadd71f8")
     version("11.7.0", sha256="6a76ae8e7682bbc790321bf80c2f9417775c5b01a5c4f10763df92e01b20b9ca")
     version("11.6.0", sha256="af4c04e0b394aa9b5f411ec5c8055888619c724768b3094727e8bb7d3ea34a54")
     version("11.5.0", sha256="d154839e29ef1fe82e58cf20232e9f8a4f0610f0e8b6a394b7ca052e58f97f43")
+    version("11.4.0", sha256="946482405e675b99e8e0c221d137768f246076f5e9ba92eed6cae47fb68b7a26")
+
+    # Patch to not add "-c" to ranlib flags when using llvm-ranlib on Apple systems
+    patch("cmakelists-apple-llvm-ranlib.patch", when="@11.5.0:11.6.0")
+    # C test does not explicity link to -lm causing DSO error when building shared libs
+    patch("c-tests-libm.patch", when="@11.5.0:11.7.0")
+    # Patch to identify Python version correctly
+    patch("python-version.patch", when="@11.5:12.0.0 +python")
+
+    variant("python", default=False, description="Enable Python interface?")
+    variant("shared", default=True, description="Build shared libraries", when="@11.5:")
+
+    extends("python", when="+python")
+
+    depends_on("python@3:", type=("build", "run"), when="+python")
+    depends_on("py-setuptools", type="build", when="+python")
+    depends_on("py-numpy", type=("build", "run"), when="+python")
+    depends_on("py-pip", type="build", when="+python")
+    depends_on("py-wheel", type="build", when="+python")
+
+    def url_for_version(self, version):
+        pre = "bufr_" if version < Version("12.0.1") else ""
+        return (
+            f"https://github.com/NOAA-EMC/NCEPLIBS-bufr/archive/refs/tags/{pre}v{version}.tar.gz"
+        )
+
+    # Need to make the lines shorter at least on some systems
+    def patch(self):
+        with when("@:11.7.1"):
+            filter_file("_lenslmax 120", "_lenslmax 60", "CMakeLists.txt")
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant("ENABLE_PYTHON", "python"),
+            self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
+            self.define("BUILD_TESTS", self.run_tests),
+        ]
+
+        return args
+
+    def flag_handler(self, name, flags):
+        """
+        On macOS if a library built with the ar utility contains objects
+        with Fortran module data but no executable functions,
+        the symbols corresponding to the module data may not be resolved
+        when an object referencing them is linked against the library.
+        You can work around this by compiling with option -fno-common.
+        """
+        fc = self.compiler.fc
+        if self.spec.satisfies("platform=darwin"):
+            if name == "fflags":
+                if "ifort" in fc or "gfortran" in fc:
+                    flags.append("-fno-common")
+
+        # Bufr inserts a path into source code which may be longer than 132
+        if name == "fflags" and "gfortran" in fc:
+            flags.append("-ffree-line-length-none")
+
+        # Inject flags into CMake build
+        return (None, None, flags)
 
     def _setup_bufr_environment(self, env, suffix):
         libname = "libbufr_{0}".format(suffix)
-        lib = find_libraries(libname, root=self.prefix, shared=False, recursive=True)
+        shared = True if "+shared" in self.spec else False
-        lib_envname = "BUFR_LIB{0}".format(suffix)
+        # Bufr has _DA (dynamic allocation) libs in versions <= 11.5.0
-        inc_envname = "BUFR_INC{0}".format(suffix)
+        append = "" if self.spec.satisfies("@11.5.0:") else "_DA"
-        include_dir = "include_{0}".format(suffix)
+        lib = find_libraries(libname + append, root=self.prefix, shared=shared, recursive=True)
+        lib_envname = "BUFR_LIB{0}".format(suffix) + append
+        inc_envname = "BUFR_INC{0}".format(suffix) + append
+        include_dir = "{0}_{1}".format(self.prefix.include.bufr, suffix)
 
         env.set(lib_envname, lib[0])
         env.set(inc_envname, include_dir)
 
-        # Bufr has _DA (dynamic allocation) libs in versions <= 11.5.0
+        if self.spec.satisfies("+python"):
-        if self.spec.satisfies("@:11.5.0"):
+            pyver = self.spec["python"].version.up_to(2)
-            da_lib = find_libraries(
+            pydir = join_path(os.path.dirname(lib[0]), f"python{pyver}", "site-packages")
-                libname + "_DA", root=self.prefix, shared=False, recursive=True
+            env.prepend_path("PYTHONPATH", pydir)
-            )
-            env.set(lib_envname + "_DA", da_lib[0])
-            env.set(inc_envname + "_DA", include_dir)
 
     def setup_run_environment(self, env):
-        for suffix in ("4", "8", "d"):
+        suffixes = ["4"]
+        if not self.spec.satisfies("@12:"):
+            suffixes += ["8", "d"]
+        for suffix in suffixes:
             self._setup_bufr_environment(env, suffix)
+
+    def check(self):
+        if self.spec.satisfies("~python"):
+            with working_dir(self.builder.build_directory):
+                make("test")

var/spack/repos/builtin/packages/bufr/python-version.patch

@@ -0,0 +1,12 @@
+--- a/python/CMakeLists.txt	2023-06-08 12:39:26.000000000 -0600
++++ b/python/CMakeLists.txt	2023-07-19 13:45:11.000000000 -0600
+@@ -8,8 +8,7 @@
+ file( COPY ncepbufr utils DESTINATION . )
+ 
+ # Library installation directory
+-execute_process(COMMAND ${Python3_EXECUTABLE} -c "from __future__ import print_function; import sys; print(sys.version[:3], end='')"
+-                  OUTPUT_VARIABLE _PYVER)
++set(_PYVER "${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}")
+ set(_install_dir "${CMAKE_INSTALL_FULL_LIBDIR}/python${_PYVER}/site-packages")
+ 
+ # Build the extension module for use in install tree