Merge pull request #510 from AlexanderRichert-NOAA/crtm_wgrib2

Update crtm(-fix), wgrib2

var/spack/repos/builtin/packages/crtm-fix/package.py

@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
@@ -18,6 +17,7 @@ class CrtmFix(Package):
         "BenjaminTJohnson", "edwardhartnett", "AlexanderRichert-NOAA", "Hang-Lei-NOAA", "climbfuji"
     )
 
+    version("3.1.1.2", sha256="c2e289f690d82a3aa82d2239cbb567cd514fa0f476a8b498ceba11670685ca66")
     version(
         "2.4.0.1_emc", sha256="6e4005b780435c8e280d6bfa23808d8f12609dfd72f77717d046d4795cac0457"
     )
@@ -27,6 +27,7 @@ class CrtmFix(Package):
     variant("big_endian", default=True, description="Install big_endian fix files")
     variant("little_endian", default=False, description="Install little endian fix files")
     variant("netcdf", default=True, description="Install netcdf fix files")
+    variant("testfiles", default=False, description="Install test files", when="@3:")
 
     conflicts("+big_endian", when="+little_endian", msg="big_endian and little_endian conflict")
 
@@ -52,7 +53,11 @@ def install(self, spec, prefix):
 
         fix_files = []
         for d in endian_dirs:
-            fix_files = fix_files + find(".", "*/{}/*".format(d))
+            fix_files = fix_files + find(".", "*/{}/*".format(d), recursive=False)
+            fix_files = fix_files + find(".", "*/*/{}/*".format(d), recursive=False)
+        if self.spec.satisfies("~testfiles"):
+            fix_files = [f for f in fix_files if "/fix/test_data/" not in f]
+        fix_files = [f for f in fix_files if os.path.isfile(f)]
 
         # Big_Endian amsua_metop-c.SpcCoeff.bin is incorrect
         # Little_Endian amsua_metop-c_v2.SpcCoeff.bin is what it's supposed to be.

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

@@ -41,6 +41,7 @@ class Crtm(CMakePackage):
     depends_on("[email protected]_emc", when="@2.3.0 +fix")
     depends_on("[email protected]_emc", when="@=2.4.0 +fix")
     depends_on("[email protected]_emc", when="@2.4.0.1 +fix")
+    depends_on("[email protected]", when="@3.1.1 +fix")
 
     depends_on("ecbuild", type=("build"), when="@v2.3-jedi.4")
     depends_on("ecbuild", type=("build"), when="@v2.4-jedi.1")
@@ -51,6 +52,9 @@ class Crtm(CMakePackage):
 
     license("CC0-1.0")
 
+    version(
+        "v3.1.1-build1", sha256="1ed49e594da5d3769cbaa52cc7fc19c1bb0325ee6324f6057227c31e2d95ca67"
+    )
     version(
         "v3.1.0-skylabv8",
         sha256="a475c8a444072aef1e8c2babba3d12f13ab0fb6c7ecab88edad57130839e29ff",
@@ -81,8 +85,9 @@ class Crtm(CMakePackage):
     depends_on("fortran", type="build")  # generated
 
     def url_for_version(self, version):
-        if self.spec.satisfies("@v3") or version >= Version("3.0.0"):
-            return f"https://github.com/JCSDA/crtmv3/archive/refs/tags/{version}.tar.gz"
+        if version > Version("v3") or version >= Version("3"):
+            fmtversion = str(version).replace("-build", "+build")
+            return f"https://github.com/JCSDA/CRTMv3/archive/refs/tags/{fmtversion}.tar.gz"
         else:
             return f"https://github.com/JCSDA/crtm/archive/refs/tags/{version}.tar.gz"
 

var/spack/repos/builtin/packages/wgrib2/package.py

@@ -1,32 +1,68 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os
 import re
 
+import spack.build_systems.cmake
+import spack.build_systems.makefile
 from spack.package import *
 
-
-class Wgrib2(MakefilePackage):
+variant_map_common = {
+    "netcdf3": "USE_NETCDF3",
+    "netcdf4": "USE_NETCDF4",
+    "mysql": "USE_MYSQL",
+    "udf": "USE_UDF",
+    "regex": "USE_REGEX",
+    "tigge": "USE_TIGGE",
+    "proj4": "USE_PROJ4",
+    "aec": "USE_AEC",
+    "g2c": "USE_G2CLIB",
+    "png": "USE_PNG",
+    "jasper": "USE_JASPER",
+    "openmp": "USE_OPENMP",
+    "wmo_validation": "USE_WMO_VALIDATION",
+    "ipolates": "USE_IPOLATES",
+    "disable_alarm": "DISABLE_ALARM",
+    "fortran_api": "MAKE_FTN_API",
+    "disable_stat": "DISABLE_STAT",
+    "openjpeg": "USE_OPENJPEG",
+}
+
+variant_map_makefile = {"spectral": "USE_SPECTRAL"}
+
+variant_map_cmake = {
+    "netcdf": "USE_NETCDF",
+    "disable_timezone": "DISABLE_TIMEZONE",
+    "enable_docs": "ENABLE_DOCS",
+}
+
+variant_map_makefile.update(variant_map_common)
+variant_map_cmake.update(variant_map_common)
+
+
+class Wgrib2(MakefilePackage, CMakePackage):
     """Utility for interacting with GRIB2 files"""
 
     homepage = "https://www.cpc.ncep.noaa.gov/products/wesley/wgrib2"
     url = "https://www.ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/wgrib2.tgz.v2.0.8"
+    git = "https://github.com/NOAA-EMC/wgrib2"
 
-    maintainers("t-brown", "AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett")
-
-    version(
-        "3.1.1",
-        sha256="9236f6afddad76d868c2cfdf5c4227f5bdda5e85ae40c18bafb37218e49bc04a",
-        extension="tar.gz",
+    maintainers(
+        "AlysonStahl-NOAA", "t-brown", "AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett"
     )
-    version(
-        "3.1.0",
-        sha256="5757ef9016b19ae87491918e0853dce2d3616b14f8c42efe3b2f41219c16b78f",
-        extension="tar.gz",
+
+    build_system(
+        conditional("cmake", when="@3.2:"), conditional("makefile", when="@:3.1"), default="cmake"
     )
+
+    version("develop", branch="develop")
+    version("3.5.0", sha256="b27b48228442a08bddc3d511d0c6335afca47252ae9f0e41ef6948f804afa3a1")
+    version("3.4.0", sha256="ecbce2209c09bd63f1bca824f58a60aa89db6762603bda7d7d3fa2148b4a0536")
+    version("3.3.0", sha256="010827fba9c31f05807e02375240950927e9e51379e1444388153284f08f58e2")
+    version("3.2.0", sha256="ac3ace77a32c2809cbc4538608ad64aabda2c9c1e44e7851da79764a6eb3c369")
+    version("3.1.1", sha256="9236f6afddad76d868c2cfdf5c4227f5bdda5e85ae40c18bafb37218e49bc04a")
+    version("3.1.0", sha256="5757ef9016b19ae87491918e0853dce2d3616b14f8c42efe3b2f41219c16b78f")
     version(
         "2.0.8",
         sha256="5e6a0d6807591aa2a190d35401606f7e903d5485719655aea1c4866cc2828160",
@@ -38,27 +74,48 @@ class Wgrib2(MakefilePackage):
         extension="tar.gz",
     )
 
-    depends_on("c", type="build")  # generated
-    depends_on("fortran", type="build")  # generated
+    def url_for_version(self, version):
+        if version >= Version("3.2.0"):
+            url_fmt = "https://github.com/NOAA-EMC/wgrib2/archive/refs/tags/v{0}.tar.gz"
+        else:
+            url_fmt = "https://www.ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/wgrib2.tgz.v{0}"
+        return url_fmt.format(version)
 
-    variant("netcdf3", default=True, description="Link in netcdf3 library to write netcdf3 files")
     variant(
-        "netcdf4", default=False, description="Link in netcdf4 library to write netcdf3/4 files"
+        "netcdf3",
+        default=True,
+        description="Link in netcdf3 library to write netcdf3 files",
+        when="@:3.1",
     )
     variant(
-        "ipolates",
-        default="3",
-        description="Use to interpolate to new grids (0 = OFF, 1 = ip, 3 = ip2)",
-        values=("0", "1", "3"),
+        "netcdf4",
+        default=False,
+        description="Link in netcdf4 library to write netcdf3/4 files",
+        when="@:3.3",
     )
-    variant("spectral", default=False, description="Spectral interpolation in -new_grid")
+    variant(
+        "netcdf",
+        default=False,
+        description="Link in netcdf4 library to write netcdf3/4 files",
+        when="@3.4:",
+    )
+    variant("ipolates", default=False, description="Use to interpolate to new grids")
+    variant(
+        "spectral", default=False, description="Spectral interpolation in -new_grid", when="@:3.1"
+    )
+    #   Not currently working for @3.2:
     variant(
         "fortran_api",
         default=True,
         description="Make wgrib2api which allows fortran code to read/write grib2",
     )
+    #   Not currently working for @3.2:
+    #    variant("lib", default=True, description="Build library", when="@3.2:")
     variant(
-        "mysql", default=False, description="Link in interface to MySQL to write to mysql database"
+        "mysql",
+        default=False,
+        description="Link in interface to MySQL to write to mysql database",
+        when="@:3.1",
     )
     variant(
         "udf",
@@ -67,11 +124,21 @@ class Wgrib2(MakefilePackage):
     )
     variant("regex", default=True, description="Use regular expression library (POSIX-2)")
     variant("tigge", default=True, description="Ability for TIGGE-like variable names")
-    variant("proj4", default=False, description="The proj4 library is used to verify gctpc.")
+    variant(
+        "proj4",
+        default=False,
+        description="The proj4 library is used to verify gctpc.",
+        when="@:3.1",
+    )
     variant(
         "aec", default=True, description="Use the libaec library for packing with GRIB2 template"
     )
-    variant("g2c", default=False, description="Include NCEP g2clib (mainly for testing purposes)")
+    variant(
+        "g2c",
+        default=False,
+        description="Include NCEP g2clib (mainly for testing purposes)",
+        when="@:3.1",
+    )
     variant(
         "disable_timezone", default=False, description="Some machines do not support timezones"
     )
@@ -84,62 +151,73 @@ class Wgrib2(MakefilePackage):
     variant("jasper", default=True, description="JPEG compression using Jasper")
     variant("openmp", default=True, description="OpenMP parallelization")
     variant("wmo_validation", default=False, description="WMO validation")
+    #    variant("shared", default=False, description="Enable shared library", when="+lib")
+    variant("disable_stat", default=False, description="Disable POSIX feature", when="@:3.1")
+    variant("openjpeg", default=False, description="Enable OpenJPEG")
+    variant(
+        "enable_docs", default=False, description="Build doxygen documentation", when="@3.4.0:"
+    )
 
     conflicts("+netcdf3", when="+netcdf4")
+    conflicts("+netcdf3", when="+netcdf")
     conflicts("+openmp", when="%apple-clang")
 
-    depends_on("wget", type=("build"), when="+netcdf4")
-    # makefile behavior with shell commands/character escapes breaks with [email protected]:
-    depends_on("gmake@:4.2")
-
-    variant_map = {
-        "netcdf3": "USE_NETCDF3",
-        "netcdf4": "USE_NETCDF4",
-        "spectral": "USE_SPECTRAL",
-        "mysql": "USE_MYSQL",
-        "udf": "USE_UDF",
-        "regex": "USE_REGEX",
-        "tigge": "USE_TIGGE",
-        "proj4": "USE_PROJ4",
-        "aec": "USE_AEC",
-        "g2c": "USE_G2CLIB",
-        "png": "USE_PNG",
-        "jasper": "USE_JASPER",
-        "openmp": "USE_OPENMP",
-        "wmo_validation": "USE_WMO_VALIDATION",
-        "ipolates": "USE_IPOLATES",
-        "disable_timezone": "DISABLE_TIMEZONE",
-        "disable_alarm": "DISABLE_ALARM",
-        "fortran_api": "MAKE_FTN_API",
-    }
-
-    # Disable parallel build
-    parallel = False
+    depends_on("[email protected]:", when="@3.5: +ipolates")
+    depends_on("lapack", when="@3.5: +ipolates")
+    depends_on("[email protected]:", when="@3.2: +aec")
+    depends_on("netcdf-c", when="@3.2: +netcdf4")
+    depends_on("jasper@:2", when="@3.2:3.4 +jasper")
+    depends_on("g2c", when="@3.5: +jasper")
+    depends_on("zlib-api", when="@3.2: +png")
+    depends_on("libpng", when="@3.2: +png")
+    depends_on("openjpeg", when="@3.2:3.4 +openjpeg")
+    depends_on("g2c +openjpeg", when="@3.5: +openjpeg")
+    requires("^[email protected]:", when="@3.5: ^g2c")
+
+    @when("@:2 ^[email protected]:")
+    def patch(self):
+        filter_file(r"\\#define", "#define", "makefile")
 
     # Use Spack compiler wrapper flags
     def inject_flags(self, name, flags):
-        spec = self.spec
         if name == "cflags":
-            if spec.satisfies("%apple-clang"):
+            if self.spec.compiler.name == "apple-clang":
                 flags.append("-Wno-error=implicit-function-declaration")
 
             # When mixing Clang/gfortran need to link to -lgfortran
             # Find this by searching for gfortran/../lib
-            if spec.satisfies("%apple-clang") or spec.satisfies("%clang"):
+            if self.spec.compiler.name in ["apple-clang", "clang"]:
                 if "gfortran" in self.compiler.fc:
                     output = Executable(self.compiler.fc)("-###", output=str, error=str)
                     libdir = re.search("--libdir=(.+?) ", output).group(1)
                     flags.append("-L{}".format(libdir))
 
         return (flags, None, None)
 
+
+class CMakeBuilder(spack.build_systems.cmake.CMakeBuilder):
+    # Disable parallel build
+    parallel = False
+
+    def cmake_args(self):
+        args = [self.define_from_variant(variant_map_cmake[k], k) for k in variant_map_cmake]
+        #        args.append(self.define_from_variant("BUILD_LIB", "lib"))
+        #        args.append(self.define_from_variant("BUILD_SHARED_LIB", "shared"))
+
+        return args
+
+
+class MakefileBuilder(spack.build_systems.makefile.MakefileBuilder):
+    # Disable parallel build
+    parallel = False
+
     flag_handler = inject_flags
 
     def url_for_version(self, version):
         url = "https://www.ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/wgrib2.tgz.v{}"
         return url.format(version)
 
-    def edit(self, spec, prefix):
+    def edit(self, pkg, spec, prefix):
         makefile = FileFilter("makefile")
 
         # ifort no longer accepts -openmp
@@ -151,31 +229,20 @@ def edit(self, spec, prefix):
         if spec.satisfies("%clang") or spec.satisfies("%apple-clang"):
             makefile.filter(r"--fast-math", "-ffast-math")
 
-        for variant_name, makefile_option in self.variant_map.items():
+        for variant_name, makefile_option in variant_map_makefile.items():
             value = int(spec.variants[variant_name].value)
             makefile.filter(r"^%s=.*" % makefile_option, "{}={}".format(makefile_option, value))
 
     def setup_build_environment(self, env):
-        spec = self.spec
-        if spec.satisfies("%oneapi") or spec.satisfies("%intel"):
+        if self.spec.compiler.name in ["oneapi", "intel"]:
             comp_sys = "intel_linux"
-        elif spec.satisfies("%gcc") or spec.satisfies("%clang") or spec.satisfies("%apple-clang"):
+        elif self.spec.compiler.name in ["gcc", "clang", "apple-clang"]:
             comp_sys = "gnu_linux"
 
         env.set("COMP_SYS", comp_sys)
 
-    def build(self, spec, prefix):
-        # Get source files for netCDF4 builds
-        if self.spec.satisfies("+netcdf4"):
-            with working_dir(self.build_directory):
-                os.system(
-                    "wget https://downloads.unidata.ucar.edu/netcdf-c/4.8.1/netcdf-c-4.8.1.tar.gz"
-                )
-                os.system(
-                    "wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/src/hdf5-1.12.1.tar.gz"
-                )
-
-        make()
+    def build(self, pkg, spec, prefix):
+        make("-j1")
 
         # Move wgrib2 executable to a tempoary directory
         mkdir("install")
@@ -190,7 +257,7 @@ def build(self, spec, prefix):
             makefile = FileFilter("makefile")
 
             # Disable all options
-            for variant_name, makefile_option in self.variant_map.items():
+            for variant_name, makefile_option in variant_map_makefile.items():
                 value = 0
                 makefile.filter(
                     r"^%s=.*" % makefile_option, "{}={}".format(makefile_option, value)
@@ -199,13 +266,13 @@ def build(self, spec, prefix):
             # Need USE_REGEX in addition to MAKE_FTN_API to build lib
             makefile.filter(r"^MAKE_FTN_API=.*", "MAKE_FTN_API=1")
             makefile.filter(r"^USE_REGEX=.*", "USE_REGEX=1")
-            make("lib")
+            make("lib", "-j1")
             mkdir(join_path("install", "lib"))
             mkdir(join_path("install", "include"))
 
             move(join_path("lib", "libwgrib2.a"), join_path("install", "lib"))
             move(join_path("lib", "wgrib2api.mod"), join_path("install", "include"))
             move(join_path("lib", "wgrib2lowapi.mod"), join_path("install", "include"))
 
-    def install(self, spec, prefix):
+    def install(self, pkg, spec, prefix):
         install_tree("install/", prefix)