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Various package updates from JCSDA spack-stack-dev: crtm, g2, grads, hdf, ip, met, metplus, py-kiwisolver, py-pyogrio, py-ruamel-yaml-clib, wgrib2 (#50108)

Browse Source 
* Update crtm from jcsda/spack-stack-dev
* Update grads from jcsda/spack-stack-dev
* Update hdf from jcsda/spack-stack-dev
* Update ip from jcsda/spack-stack-dev
* Update met from jcsda/spack-stack-dev
* Update metplus from jcsda/spack-stack-dev
* Update py-kiwisolver from jcsda/spack-stack-dev
* Update py-pyogrio from jcsda/spack-stack-dev
* Update py-ruamel-yaml-clib from jcsda/spack-stack-dev
* Update wgrib2 from jcsda/spack-stack-dev
This commit is contained in:
Dom Heinzeller 2025-05-15 15:19:57 -06:00 committed by GitHub
parent ac08428f20
commit 7f8c5bd4ca
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
11 changed files with 57 additions and 11 deletions
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15
var/spack/repos/spack_repo/builtin/packages/crtm/package.py
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@ -2,6 +2,9 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import glob
import os
from spack.package import *
@ -40,6 +43,7 @@ class Crtm(CMakePackage):
depends_on("crtm-fix@2.3.0_emc", when="@2.3.0 +fix")
depends_on("crtm-fix@2.4.0_emc", when="@=2.4.0 +fix")
depends_on("crtm-fix@2.4.0.1_emc", when="@2.4.0.1 +fix")
depends_on("crtm-fix@3.1.1", 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")
@ -51,7 +55,7 @@ class Crtm(CMakePackage):
license("CC0-1.0")
version(
"v3.1.1-build1", sha256="1ed49e594da5d3769cbaa52cc7fc19c1bb0325ee6324f6057227c31e2d95ca67"
"3.1.1-build1", sha256="1ed49e594da5d3769cbaa52cc7fc19c1bb0325ee6324f6057227c31e2d95ca67"
)
version(
"v3.1.0-skylabv8",
@ -85,6 +89,8 @@ class Crtm(CMakePackage):
def url_for_version(self, version):
if version > Version("v3") or version >= Version("3"):
fmtversion = str(version).replace("-build", "+build")
if not fmtversion.startswith("v"):
fmtversion = f"v{fmtversion}"
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"
@ -101,3 +107,10 @@ def patch(self):
)
if not self.run_tests:
filter_file(r"add_subdirectory\(test\)", "# disable testing", "CMakeLists.txt")
@when("@3.1.1-build1")
@run_after("install")
def cmake_config_softlinks(self):
cmake_config_files = glob.glob(join_path(self.prefix, "cmake/crtm/*"))
for srcpath in cmake_config_files:
os.symlink(srcpath, join_path(self.prefix, "cmake", os.path.basename(srcpath)))

4
var/spack/repos/spack_repo/builtin/packages/grads/package.py
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@ -25,7 +25,7 @@ class Grads(AutotoolsPackage):
variant("geotiff", default=True, description="Enable GeoTIFF support")
variant("shapefile", default=True, description="Enable Shapefile support")
variant("grib2", default=True, description="Enable GRIB2 support")
variant("grib2", default=True, description="Enable GRIB2 support with the g2c library.")
variant("dap", default=False, description="Enable DAP support")
# TODO: This variant depends on the "simple X" library, which is no longer available
@ -43,7 +43,7 @@ class Grads(AutotoolsPackage):
depends_on("hdf5", when="+hdf5")
depends_on("hdf", when="+hdf4")
depends_on("netcdf-c", when="+netcdf")
depends_on("g2c", when="+grib2")
depends_on("g2c+pic", when="+grib2")
depends_on("libgeotiff", when="+geotiff")
depends_on("shapelib", when="+shapefile")
depends_on("gadap", when="+dap")

12
var/spack/repos/spack_repo/builtin/packages/hdf/package.py
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@ -96,7 +96,7 @@ class Hdf(AutotoolsPackage):
sha256="49733dd6143be7b30a28d386701df64a72507974274f7e4c0a9e74205510ea72",
when="@4.2.15:",
)
# https://github.com/NOAA-EMC/spack-stack/issues/317
# https://github.com/jcsda/spack-stack/issues/317
patch("hdfi_h_apple_m1.patch", when="@4.2.15: target=aarch64: platform=darwin")
@property
@ -160,6 +160,7 @@ def flag_handler(self, name, flags):
if (
self.spec.satisfies("%clang@16:")
or self.spec.satisfies("%apple-clang@15:")
or self.spec.satisfies("%oneapi")
or self.spec.satisfies("%gcc@14:")
):
flags.append("-Wno-error=implicit-int")
@ -218,6 +219,15 @@ def cached_tests_work_dir(self):
"""The working directory for cached test sources."""
return join_path(self.test_suite.current_test_cache_dir, self.extra_install_tests)
@run_after("install")
def remove_ncgen_ncdump(self):
"""Remove binaries ncdump and ncgen. These get built and
installed even if the netCDF API is turned off (known bug)."""
if self.spec.satisfies("~netcdf"):
exes_to_remove = ["ncdump", "ncgen"]
for exe in exes_to_remove:
os.remove(os.path.join(self.prefix.bin, exe))
@run_after("install")
def setup_build_tests(self):
"""Copy the build test files after the package is installed to an

2
var/spack/repos/spack_repo/builtin/packages/ip/package.py
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@ -17,6 +17,8 @@ class Ip(CMakePackage):
maintainers("AlexanderRichert-NOAA", "edwardhartnett", "Hang-Lei-NOAA")
version("develop", branch="develop")
version("5.3.0", sha256="17dfcb52bab58d3f1bcbbdda5e76430020d963097139e1ba240bfc5fb5c5a5d1")
version("5.2.0", sha256="2f7b44abcf24e448855f57d107db55d3d58cbc271164ba083491d0c07a7ea3d0")
version("5.1.0", sha256="5279f11f4c12db68ece74cec392b7a2a6b5166bc505877289f34cc3149779619")
version("5.0.0", sha256="54b2987bd4f94adc1f7595d2a384e646019c22d163bcd30840a916a6abd7df71")
version("4.4.0", sha256="858d9201ce0bc4d16b83581ef94a4a0262f498ed1ea1b0535de2e575da7a8b8c")

8
var/spack/repos/spack_repo/builtin/packages/met/package.py
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@ -16,7 +16,7 @@ class Met(AutotoolsPackage):
url = "https://github.com/dtcenter/MET/archive/refs/tags/v11.0.1.tar.gz"
git = "https://github.com/dtcenter/MET"
maintainers("AlexanderRichert-NOAA")
maintainers("AlexanderRichert-NOAA", "climbfuji")
version("develop", branch="develop")
version("12.0.1", sha256="ef396a99ca6c2248855848cd194f9ceaf3b051fb5e8c01a0b0b2a00110b1fcfb")
@ -67,10 +67,8 @@ class Met(AutotoolsPackage):
patch("openmp_shape_patch.patch", when="@10.1.0")
# https://github.com/JCSDA/spack-stack/issues/615
# TODO(srherbener) Apple clang 14.x is getting pickier! When these updates are
# merged into the MET code base, the following two patches can be removed.
patch("apple-clang-string-cast-operator.patch", when="@10.1.1: %apple-clang@14:")
patch("apple-clang-no-register.patch", when="@10.1.1: %apple-clang@14:")
patch("apple-clang-string-cast-operator.patch", when="@10.1.1:11.0 %apple-clang@14:")
patch("apple-clang-no-register.patch", when="@10.1.1:11.0 %apple-clang@14:")
def url_for_version(self, version):
if version < Version("11"):

2
var/spack/repos/spack_repo/builtin/packages/metplus/package.py
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@ -15,7 +15,7 @@ class Metplus(Package):
url = "https://github.com/dtcenter/METplus/archive/refs/tags/v4.1.0.tar.gz"
git = "https://github.com/dtcenter/METplus"
maintainers("AlexanderRichert-NOAA")
maintainers("AlexanderRichert-NOAA", "climbfuji")
version("develop", branch="develop")
version("6.0.0", sha256="e9358aede2fd2abecd81806227de7b165d68fdf2fc9defcbba24df229461b155")

15
var/spack/repos/spack_repo/builtin/packages/py_kiwisolver/macos-gcc.patch Normal file
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@ -0,0 +1,15 @@
--- a/setup.py 2022-04-19 20:56:49.000000000 -0600
+++ b/setup.py 2022-04-19 20:58:52.000000000 -0600
@@ -54,9 +54,9 @@
for ext in self.extensions:
ext.include_dirs.insert(0, cppy.get_include())
ext.extra_compile_args = opts
- if sys.platform == 'darwin':
- ext.extra_compile_args += ['-stdlib=libc++']
- ext.extra_link_args += ['-stdlib=libc++']
+ #if sys.platform == 'darwin':
+ # ext.extra_compile_args += ['-stdlib=libc++']
+ # ext.extra_link_args += ['-stdlib=libc++']
if (ct == 'msvc' and os.environ.get('KIWI_DISABLE_FH4')):
# Disable FH4 Exception Handling implementation so that we don't
# require VCRUNTIME140_1.dll. For more details, see:

4
var/spack/repos/spack_repo/builtin/packages/py_kiwisolver/package.py
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@ -38,3 +38,7 @@ class PyKiwisolver(PythonPackage):
depends_on("py-cppy@1.2.0:", type="build", when="@1.4.4:")
depends_on("py-cppy@1.3.0:", type="build", when="@1.4.8:")
depends_on("py-typing-extensions", when="@1.4.4: ^python@:3.7", type=("build", "run"))
# https://github.com/spack/spack/issues/28522
# https://github.com/nucleic/kiwi/issues/126
patch("macos-gcc.patch", when="@:1.3.2 platform=darwin %gcc")

2
var/spack/repos/spack_repo/builtin/packages/py_pyogrio/package.py
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@ -19,6 +19,8 @@ class PyPyogrio(PythonPackage):
version("0.9.0", sha256="6a6fa2e8cf95b3d4a7c0fac48bce6e5037579e28d3eb33b53349d6e11f15e5a8")
depends_on("python@3.8:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-wheel", type="build")
depends_on("gdal@2.4:", type=("build", "link", "run"))
depends_on("py-cython@0.29:", type="build")
depends_on("py-versioneer@0.28 +toml", type="build")

1
var/spack/repos/spack_repo/builtin/packages/py_ruamel_yaml_clib/package.py
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@ -16,6 +16,7 @@ class PyRuamelYamlClib(PythonPackage):
version("0.2.12", sha256="6c8fbb13ec503f99a91901ab46e0b07ae7941cd527393187039aec586fdfd36f")
version("0.2.7", sha256="1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497")
version("0.2.4", sha256="f997f13fd94e37e8b7d7dbe759088bb428adc6570da06b64a913d932d891ac8d")
with default_args(deprecated=True):
version("0.2.0", sha256="b66832ea8077d9b3f6e311c4a53d06273db5dc2db6e8a908550f3c14d67e718c")

3
var/spack/repos/spack_repo/builtin/packages/wgrib2/package.py
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@ -57,6 +57,7 @@ class Wgrib2(MakefilePackage, CMakePackage):
)
version("develop", branch="develop")
version("3.6.0", sha256="55913cb58f2b329759de17f5a84dd97ad1844d7a93956d245ec94f4264d802be")
version("3.5.0", sha256="b27b48228442a08bddc3d511d0c6335afca47252ae9f0e41ef6948f804afa3a1")
version("3.4.0", sha256="ecbce2209c09bd63f1bca824f58a60aa89db6762603bda7d7d3fa2148b4a0536")
version("3.3.0", sha256="010827fba9c31f05807e02375240950927e9e51379e1444388153284f08f58e2")
@ -192,7 +193,7 @@ def patch(self):
# Use Spack compiler wrapper flags
def inject_flags(self, name, flags):
if name == "cflags":
if self.spec.compiler.name == "apple-clang":
if self.spec.compiler.name in ["apple-clang", "clang"]:
flags.append("-Wno-error=implicit-function-declaration")
# When mixing Clang/gfortran need to link to -lgfortran