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# 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)
import os
import sys
from spack.package import *
class Hdf(AutotoolsPackage):
"""HDF4 (also known as HDF) is a library and multi-object
file format for storing and managing data between machines."""
homepage = "https://portal.hdfgroup.org"
url = "https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.14/src/hdf-4.2.14.tar.gz"
list_url = "https://support.hdfgroup.org/ftp/HDF/releases/"
list_depth = 2
maintainers("lrknox")
version("4.2.15", sha256="dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459")
version("4.2.14", sha256="2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a")
version("4.2.13", sha256="be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483")
version("4.2.12", sha256="dd419c55e85d1a0e13f3ea5ed35d00710033ccb16c85df088eb7925d486e040c")
version("4.2.11", sha256="c3f7753b2fb9b27d09eced4d2164605f111f270c9a60b37a578f7de02de86d24")
variant("szip", default=False, description="Enable szip support")
variant(
"external-xdr", default=sys.platform != "darwin", description="Use an external XDR backend"
)
variant("netcdf", default=False, description="Build NetCDF API (version 2.3.2)")
variant("fortran", default=False, description="Enable Fortran interface")
variant("java", default=False, description="Enable Java JNI interface")
variant("shared", default=False, description="Enable shared library")
variant("pic", default=True, description="Produce position-independent code")
depends_on("zlib-api")
depends_on("jpeg")
depends_on("szip", when="+szip")
depends_on("rpc", when="+external-xdr")
depends_on("bison", type="build")
depends_on("flex", type="build")
depends_on("java@7:", when="+java", type=("build", "run"))
# https://forum.hdfgroup.org/t/cant-build-hdf-4-2-14-with-jdk-11-and-enable-java/5702
patch("disable_doclint.patch", when="@:4.2.14^java@9:")
conflicts("^libjpeg@:6a")
# configure: error: Cannot build shared fortran libraries.
# Please configure with --disable-fortran flag.
conflicts("+fortran", when="+shared")
# configure: error: Java requires shared libraries to be built
conflicts("+java", when="~shared")
# configure: WARNING: unrecognized options: --enable-java
conflicts("+java", when="@:4.2.11")
# The Java interface library uses netcdf-related macro definitions even
# when netcdf is disabled and the macros are not defined, e.g.:
# hdfsdsImp.c:158:30: error: 'MAX_NC_NAME' undeclared
conflicts("+java", when="@4.2.12:4.2.13~netcdf")
# TODO: '@:4.2.14 ~external-xdr' and the fact that we compile for 64 bit
# architecture should be in conflict
# https://github.com/knedlsepp/nixpkgs/commit/c1a2918c849a5bc766c6d55d96bc6cf85c9d27f4
patch(
"https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-ppc.patch?full_index=1",
sha256="5434f29a87856aa05124c7a9409b3ec3106c30b1ad722720773623190f6bfda8",
when="@4.2.15:",
)
patch(
"https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-4.2.4-sparc.patch?full_index=1",
sha256="ce75518cccbeb80ab976b299225ea6104c3eec1ec13c09e2289913279fcf1b39",
when="@4.2.15:",
)
patch(
"https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-s390.patch?full_index=1",
sha256="f7d67e8c3d0dad8bfca308936c6ac917cc0b63222c6339a29efdce14e8be6475",
when="@4.2.15:",
)
patch(
"https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-arm.patch?full_index=1",
sha256="d54592df281c92e7e655b8312d18bef9ed096848de9430510e0699e98246ccd3",
when="@4.2.15:",
)
patch(
"https://src.fedoraproject.org/rpms/hdf/raw/edbe5f49646b609f5bc9aeeee5a2be47e9556e8c/f/hdf-aarch64.patch?full_index=1",
sha256="49733dd6143be7b30a28d386701df64a72507974274f7e4c0a9e74205510ea72",
when="@4.2.15:",
)
# https://github.com/NOAA-EMC/spack-stack/issues/317
patch("hdfi_h_apple_m1.patch", when="@4.2.15: target=aarch64: platform=darwin")
@property
def libs(self):
"""HDF can be queried for the following parameters:
- "shared": shared libraries (default if '+shared')
- "static": static libraries (default if '~shared')
- "transitive": append transitive dependencies to the list of static
libraries (the argument is ignored if shared libraries are
requested)
:return: list of matching libraries
"""
libraries = ["libmfhdf", "libdf"]
query_parameters = self.spec.last_query.extra_parameters
if "shared" in query_parameters:
shared = True
elif "static" in query_parameters:
shared = False
else:
shared = "+shared" in self.spec
libs = find_libraries(libraries, root=self.prefix, shared=shared, recursive=True)
if not libs:
msg = "Unable to recursively locate {0} {1} libraries in {2}"
raise spack.error.NoLibrariesError(
msg.format("shared" if shared else "static", self.spec.name, self.spec.prefix)
)
if not shared and "transitive" in query_parameters:
libs += self.spec["jpeg:transitive"].libs
libs += self.spec["zlib:transitive"].libs
if "+szip" in self.spec:
libs += self.spec["szip:transitive"].libs
if "+external-xdr" in self.spec and self.spec["rpc"].name != "libc":
libs += self.spec["rpc:transitive"].libs
return libs
def flag_handler(self, name, flags):
if "+pic" in self.spec:
if name == "cflags":
flags.append(self.compiler.cc_pic_flag)
elif name == "fflags":
flags.append(self.compiler.f77_pic_flag)
if name == "cflags":
# https://forum.hdfgroup.org/t/help-building-hdf4-with-clang-error-implicit-declaration-of-function-test-mgr-szip-is-invalid-in-c99/7680
if self.spec.satisfies("@:4.2.15 %apple-clang") or self.spec.satisfies("%clang@16:"):
flags.append("-Wno-error=implicit-function-declaration")
if self.spec.satisfies("%clang@16:"):
flags.append("-Wno-error=implicit-int")
return flags, None, None
def configure_args(self):
config_args = [
"--enable-production",
"--enable-static",
"--with-zlib=%s" % self.spec["zlib-api"].prefix,
"--with-jpeg=%s" % self.spec["jpeg"].prefix,
]
config_args += self.enable_or_disable("shared")
config_args += self.enable_or_disable("netcdf")
config_args += self.enable_or_disable("fortran")
config_args += self.enable_or_disable("java")
if "+szip" in self.spec:
config_args.append("--with-szlib=%s" % self.spec["szip"].prefix)
else:
config_args.append("--without-szlib")
if "~external-xdr" in self.spec:
config_args.append("--enable-hdf4-xdr")
elif self.spec["rpc"].name != "libc":
# We should not specify '--disable-hdf4-xdr' due to a bug in the
# configure script.
config_args.append("LIBS=%s" % self.spec["rpc"].libs.link_flags)
config_args.append("LDFLAGS=%s" % self.spec["rpc"].libs.search_flags)
# https://github.com/Parallel-NetCDF/PnetCDF/issues/61
if self.spec.satisfies("%gcc@10:"):
config_args.extend(
["FFLAGS=-fallow-argument-mismatch", "FCFLAGS=-fallow-argument-mismatch"]
)
return config_args
# Otherwise, we randomly get:
# SDgetfilename:
# incorrect file being opened - expected <file755>, retrieved <file754>
def check(self):
with working_dir(self.build_directory):
make("check", parallel=False)
extra_install_tests = join_path("hdf", "util", "testfiles")
# Filter h4cc compiler wrapper to substitute the Spack compiler
# wrappers with the path of the underlying compilers.
filter_compiler_wrappers("h4cc", relative_root="bin")
@property
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 setup_build_tests(self):
"""Copy the build test files after the package is installed to an
install test subdirectory for use during `spack test run`."""
self.cache_extra_test_sources(self.extra_install_tests)
def _check_version_match(self, exe):
"""Ensure exe version check yields spec version."""
path = join_path(self.prefix.bin, exe)
if not os.path.isfile(path):
raise SkipTest(f"{exe} is not installed")
exe = which(path)
out = exe("-V", output=str.split, error=str.split)
vers = f"Version {self.spec.version.up_to(2)}"
assert vers in out
def test_hdfimport_version(self):
"""ensure hdfimport version matches spec"""
self._check_version_match("hdfimport")
def test_hrepack_version(self):
"""ensure hrepack version matches spec"""
self._check_version_match("hrepack")
def test_ncdump_version(self):
"""ensure ncdump version matches spec"""
self._check_version_match("hrepack")
def test_ncgen_version(self):
"""ensure ncgen version matches spec"""
self._check_version_match("ncgen")
def test_gif_converters(self):
"""test image conversion sequence and diff"""
base_name = "storm110"
storm_fn = join_path(self.cached_tests_work_dir, f"{base_name}.hdf")
if not os.path.exists(storm_fn):
raise SkipTest(f"Missing test image {storm_fn}")
if not os.path.exists(self.prefix.bin.hdf2gif) or not os.path.exists(
self.prefix.bin.gif2hdf
):
raise SkipTest("Missing one or more installed: 'hdf2gif', 'gif2hdf'")
gif_fn = f"{base_name}.gif"
new_hdf_fn = f"{base_name}gif.hdf"
with test_part(
self, "test_gif_converters_hdf2gif", purpose=f"convert {base_name} hdf-to-gif"
):
hdf2gif = which(self.prefix.bin.hdf2gif)
hdf2gif(storm_fn, gif_fn)
with test_part(
self, "test_gif_converters_gif2hdf", purpose=f"convert {base_name} gif-to-hdf"
):
gif2hdf = which(self.prefix.bin.gif2hdf)
gif2hdf(gif_fn, new_hdf_fn)
with test_part(
self, "test_gif_converters_hdiff", purpose=f"compare new and orig {base_name} hdf"
):
hdiff = which(self.prefix.bin.hdiff)
hdiff(new_hdf_fn, storm_fn)
def test_list(self):
"""compare low-level HDF file information to expected"""
base_name = "storm110"
if not os.path.isfile(self.prefix.bin.hdfls):
raise SkipTest("hdfls is not installed")
test_data_dir = self.test_suite.current_test_data_dir
details_file = os.path.join(test_data_dir, f"{base_name}.out")
expected = get_escaped_text_output(details_file)
storm_fn = os.path.join(self.cached_tests_work_dir, f"{base_name}.hdf")
hdfls = which(self.prefix.bin.hdfls)
out = hdfls(storm_fn, output=str.split, error=str.split)
check_outputs(expected, out)
|
