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18c2f1a57a69224748e091e912851317d8a00eea
spack/var/spack/repos/tutorial/packages/hdf5/package.py
Tom Scogland 18c2f1a57a refactor: packages import spack.package explicitly (#30404) 
Explicitly import package utilities in all packages, and corresponding fallout.

This includes:

* rename `spack.package` to `spack.package_base`
* rename `spack.pkgkit` to `spack.package`
* update all packages in builtin, builtin_mock and tutorials to include `from spack.package import *`
* update spack style
  * ensure packages include the import
  * automatically add the new import and remove any/all imports of `spack` and `spack.pkgkit`
    from packages when using `--fix`
  * add support for type-checking packages with mypy when SPACK_MYPY_CHECK_PACKAGES
    is set in the environment
* fix all type checking errors in packages in spack upstream
* update spack create to include the new imports
* update spack repo to inject the new import, injection persists to allow for a deprecation period

Original message below:
 
As requested @adamjstewart, update all packages to use pkgkit.  I ended up using isort to do this,
so repro is easy:

```console
$ isort -a 'from spack.pkgkit import *' --rm 'spack' ./var/spack/repos/builtin/packages/*/package.py
$ spack style --fix
```

There were several line spacing fixups caused either by space manipulation in isort or by packages
that haven't been touched since we added requirements, but there are no functional changes in here.

* [x] add config to isort to make sure this is maintained going forward
2022-05-28 12:55:44 -04:00

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# Copyright 2013-2022 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 shutil
import sys
import llnl.util.tty as tty
from spack.package import *
class Hdf5(CMakePackage):
"""HDF5 is a data model, library, and file format for storing and managing
data. It supports an unlimited variety of datatypes, and is designed for
flexible and efficient I/O and for high volume and complex data.
"""
homepage = "https://portal.hdfgroup.org"
url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7.tar.gz"
list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
list_depth = 3
git = "https://github.com/HDFGroup/hdf5.git"
maintainers = ['lrknox', 'brtnfld', 'byrnHDF', 'ChristopherHogan', 'epourmal',
'gheber', 'hyoklee', 'lkurz', 'soumagne']
test_requires_compiler = True
# The 'develop' version is renamed so that we could uninstall (or patch) it
# without affecting other develop version.
version('develop-1.13', branch='develop')
version('develop-1.12', branch='hdf5_1_12')
version('develop-1.10', branch='hdf5_1_10')
version('develop-1.8', branch='hdf5_1_8')
version('1.12.1', sha256='79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca')
version('1.12.0', sha256='a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a')
# HDF5 1.12 broke API compatibility, so we currently prefer the latest
# 1.10 release. packages that want later versions of HDF5 should specify,
# e.g., depends_on("hdf5@1.12:") to get 1.12 or higher.
version('1.10.7', sha256='7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15', preferred=True)
version('1.10.6', sha256='5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa')
version('1.10.5', sha256='6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8')
version('1.10.4', sha256='8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2')
version('1.10.3', sha256='b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
version('1.10.2', sha256='bfec1be8c366965a99812cf02ddc97e4b708c1754fccba5414d4adccdc073866')
version('1.10.1', sha256='048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172')
version('1.10.0-patch1', sha256='6e78cfe32a10e6e0629393cdfddf6cfa536571efdaf85f08e35326e1b4e9eff0')
version('1.10.0', sha256='81f6201aba5c30dced5dcd62f5d5477a2790fd5850e02ac514ca8bf3e2bb375a')
version('1.8.22', sha256='8406d96d9355ef8961d2739fb8fd5474ad4cdf52f3cfac657733defd9709bfaa')
version('1.8.21', sha256='87d8c82eba5cf766d97cd06c054f4639c1049c4adeaa3a79f77f8bd374f80f37')
version('1.8.19', sha256='a4335849f19fae88c264fd0df046bc321a78c536b2548fc508627a790564dc38')
version('1.8.18', sha256='cdb195ad8d9e6782acf24b2488061289f615628c2ccda8457b0a0c3fb7a8a063')
version('1.8.17', sha256='d9cda297ee76ade9881c4208987939250d397bae6252d0ccb66fa7d24d67e263')
version('1.8.16', sha256='ed17178abd9928a7237f30370189ba767b9e39e0db45917c2ac4665eb9cb4771')
version('1.8.15', sha256='4e963216b7d32469596bc1321a8c3f6e0c278dcbbdb7be6414c63c081b34c275')
version('1.8.14', sha256='1dbefeeef7f591897c632b2b090db96bb8d35ad035beaa36bc39cb2bc67e0639')
version('1.8.13', sha256='82f6b38eec103b4fccfbf14892786e0c27a8135d3252d8601cf5bf20066d38c1')
version('1.8.12', sha256='b5cccea850096962b5fd9e96f22c4f47d2379224bb41130d9bc038bb6c37dfcb')
version('1.8.10', sha256='4813b79c5fb8701a625b9924b8203bc7154a77f9b826ad4e034144b4056a160a')
variant('shared', default=True,
description='Builds a shared version of the library')
variant('hl', default=False, description='Enable the high-level library')
variant('cxx', default=False, description='Enable C++ support')
variant('fortran', default=False, description='Enable Fortran support')
variant('java', default=False, description='Enable Java support')
variant('threadsafe', default=False,
description='Enable thread-safe capabilities')
variant('tools', default=True, description='Enable building tools')
variant('mpi', default=True, description='Enable MPI support')
variant('szip', default=False, description='Enable szip support')
# Build HDF5 with API compatibility.
variant('api', default='default',
description='Choose api compatibility for earlier version',
values=('default', 'v114', 'v112', 'v110', 'v18', 'v16'),
multi=False)
depends_on('cmake@3.12:', type='build')
depends_on('mpi', when='+mpi')
depends_on('java', type=('build', 'run'), when='+java')
# numactl does not currently build on darwin
if sys.platform != 'darwin':
depends_on('numactl', when='+mpi+fortran')
depends_on('szip', when='+szip')
depends_on('zlib@1.1.2:')
# The compiler wrappers (h5cc, h5fc, etc.) run 'pkg-config'.
depends_on('pkgconfig', type='run')
conflicts('api=v114', when='@1.6.0:1.12',
msg='v114 is not compatible with this release')
conflicts('api=v112', when='@1.6.0:1.10',
msg='v112 is not compatible with this release')
conflicts('api=v110', when='@1.6.0:1.8',
msg='v110 is not compatible with this release')
conflicts('api=v18', when='@1.6.0:1.6',
msg='v18 is not compatible with this release')
# The Java wrappers and associated libhdf5_java library
# were first available in 1.10
conflicts('+java', when='@:1.9')
# The Java wrappers cannot be built without shared libs.
conflicts('+java', when='~shared')
# There are several officially unsupported combinations of the features:
# 1. Thread safety is not guaranteed via high-level C-API but in some cases
# it works.
# conflicts('+threadsafe+hl')
# 2. Thread safety is not guaranteed via Fortran (CXX) API, but it's
# possible for a dependency tree to contain a package that uses Fortran
# (CXX) API in a single thread and another one that uses low-level C-API
# in multiple threads. To allow for such scenarios, we don't specify the
# following conflicts.
# conflicts('+threadsafe+cxx')
# conflicts('+threadsafe+fortran')
# 3. Parallel features are not supported via CXX API, but for the reasons
# described in #2 we allow for such combination.
# conflicts('+mpi+cxx')
# There are known build failures with intel@18.0.1. This issue is
# discussed and patch is provided at
# https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
patch('h5f90global-mult-obj-same-equivalence-same-common-block.patch',
when='@1.10.1%intel@18')
# Turn line comments into block comments to conform with pre-C99 language
# standards. Versions of hdf5 after 1.8.10 don't require this patch,
# either because they conform to pre-C99 or neglect to ask for pre-C99
# language standards from their compiler. The hdf5 build system adds
# the -ansi cflag (run 'man gcc' for info on -ansi) for some versions
# of some compilers (see hdf5-1.8.10/config/gnu-flags). The hdf5 build
# system does not provide an option to disable -ansi, but since the
# pre-C99 code is restricted to just five lines of line comments in
# three src files, this patch accomplishes the simple task of patching the
# three src files and leaves the hdf5 build system alone.
patch('pre-c99-comments.patch', when='@1.8.10')
# There are build errors with GCC 8, see
# https://forum.hdfgroup.org/t/1-10-2-h5detect-compile-error-gcc-8-1-0-on-centos-7-2-solved/4441
patch('https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch',
sha256='57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523',
when='@1.10.2%gcc@8:')
# Disable MPI C++ interface when C++ is disabled, otherwise downstream
# libraries fail to link; see https://github.com/spack/spack/issues/12586
patch('h5public-skip-mpicxx.patch', when='@1.8.10:1.8.21,1.10.0:1.10.5+mpi~cxx',
sha256='b61e2f058964ad85be6ee5ecea10080bf79e73f83ff88d1fa4b602d00209da9c')
# Fixes BOZ literal constant error when compiled with GCC 10.
# The issue is described here: https://github.com/spack/spack/issues/18625
patch('hdf5_1.8_gcc10.patch', when='@:1.8.21',
sha256='0e20187cda3980a4fdff410da92358b63de7ebef2df1d7a425371af78e50f666')
# The argument 'buf_size' of the C function 'h5fget_file_image_c' is
# declared as intent(in) though it is modified by the invocation. As a
# result, aggressive compilers such as Fujitsu's may do a wrong
# optimization to cause an error.
def patch(self):
filter_file(
'INTEGER(SIZE_T), INTENT(IN) :: buf_size',
'INTEGER(SIZE_T), INTENT(OUT) :: buf_size',
'fortran/src/H5Fff.F90',
string=True, ignore_absent=True)
filter_file(
'INTEGER(SIZE_T), INTENT(IN) :: buf_size',
'INTEGER(SIZE_T), INTENT(OUT) :: buf_size',
'fortran/src/H5Fff_F03.f90',
string=True, ignore_absent=True)
# The parallel compiler wrappers (i.e. h5pcc, h5pfc, etc.) reference MPI
# compiler wrappers and do not need to be changed.
filter_compiler_wrappers('h5cc', 'h5hlcc',
'h5fc', 'h5hlfc',
'h5c++', 'h5hlc++',
relative_root='bin')
def url_for_version(self, version):
url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
return url.format(version.up_to(2), version)
def flag_handler(self, name, flags):
cmake_flags = []
if name == "cflags":
if self.spec.satisfies('%gcc') \
or self.spec.satisfies('%clang'):
# Quiet warnings/errors about implicit declaration of functions
# in C99:
cmake_flags.append("-Wno-implicit-function-declaration")
# Note that this flag will cause an error if building %nvhpc.
if self.spec.satisfies('@:1.8.12~shared'):
# More recent versions set CMAKE_POSITION_INDEPENDENT_CODE to
# True and build with PIC flags.
cmake_flags.append(self.compiler.cc_pic_flag)
elif name == 'cxxflags':
if self.spec.satisfies('@:1.8.12+cxx~shared'):
cmake_flags.append(self.compiler.cxx_pic_flag)
elif name == "fflags":
if self.spec.satisfies('@:1.8.12+fortran~shared'):
cmake_flags.append(self.compiler.fc_pic_flag)
elif name == "ldlibs":
if '+fortran %fj' in self.spec:
cmake_flags.extend(['-lfj90i', '-lfj90f',
'-lfjsrcinfo', '-lelf'])
return flags, None, (cmake_flags or None)
@property
def libs(self):
"""HDF5 can be queried for the following parameters:
- "hl": high-level interface
- "cxx": C++ APIs
- "fortran": Fortran APIs
- "java": Java APIs
:return: list of matching libraries
"""
query_parameters = self.spec.last_query.extra_parameters
shared = '+shared' in self.spec
# This map contains a translation from query_parameters
# to the libraries needed
query2libraries = {
tuple(): ['libhdf5'],
('cxx', 'fortran', 'hl', 'java'): [
# When installed with Autotools, the basename of the real
# library file implementing the High-level Fortran interface is
# 'libhdf5hl_fortran'. Starting versions 1.8.22, 1.10.5 and
# 1.12.0, the Autotools installation also produces a symbolic
# link 'libhdf5_hl_fortran.<so/a>' to
# 'libhdf5hl_fortran.<so/a>'. Note that in the case of the
# dynamic library, the latter is a symlink to the real sonamed
# file 'libhdf5_fortran.so.<abi-version>'. This means that all
# dynamically linked executables/libraries of the dependent
# packages need 'libhdf5_fortran.so.<abi-version>' with the same
# DT_SONAME entry. However, the CMake installation (at least
# starting version 1.8.10) does not produce it. Instead, the
# basename of the library file is 'libhdf5_hl_fortran'. Which
# means that switching to CMake requires rebuilding of all
# dependant packages that use the High-level Fortran interface.
# Therefore, we do not try to preserve backward compatibility
# with Autotools installations by creating symlinks. The only
# packages that could benefit from it would be those that
# hardcode the library name in their building systems. Such
# packages should simply be patched.
'libhdf5_hl_fortran',
'libhdf5_hl_f90cstub',
'libhdf5_hl_cpp',
'libhdf5_hl',
'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5_java',
'libhdf5',
],
('cxx', 'hl'): [
'libhdf5_hl_cpp',
'libhdf5_hl',
'libhdf5',
],
('fortran', 'hl'): [
'libhdf5_hl_fortran',
'libhdf5_hl_f90cstub',
'libhdf5_hl',
'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5',
],
('hl',): [
'libhdf5_hl',
'libhdf5',
],
('cxx', 'fortran'): [
'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5_cpp',
'libhdf5',
],
('cxx',): [
'libhdf5_cpp',
'libhdf5',
],
('fortran',): [
'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5',
],
('java',): [
'libhdf5_java',
'libhdf5',
]
}
# Turn the query into the appropriate key
key = tuple(sorted(query_parameters))
libraries = query2libraries[key]
return find_libraries(
libraries, root=self.prefix, shared=shared, recursive=True
)
@when('@:1.8.21,1.10.0:1.10.5+szip')
def setup_build_environment(self, env):
env.set('SZIP_INSTALL', self.spec['szip'].prefix)
@run_before('cmake')
def fortran_check(self):
if '+fortran' in self.spec and not self.compiler.fc:
msg = 'cannot build a Fortran variant without a Fortran compiler'
raise RuntimeError(msg)
def cmake_args(self):
spec = self.spec
if spec.satisfies('@:1.8.15+shared'):
tty.warn('hdf5@:1.8.15+shared does not produce static libraries')
args = [
# Always enable this option. This does not actually enable any
# features: it only *allows* the user to specify certain
# combinations of other arguments.
self.define('ALLOW_UNSUPPORTED', True),
# Speed-up the building by skipping the examples:
self.define('HDF5_BUILD_EXAMPLES', False),
self.define(
'BUILD_TESTING',
self.run_tests or
# Version 1.8.22 fails to build the tools when shared libraries
# are enabled but the tests are disabled.
spec.satisfies('@1.8.22+shared+tools')),
self.define('HDF5_ENABLE_Z_LIB_SUPPORT', True),
self.define_from_variant('HDF5_ENABLE_SZIP_SUPPORT', 'szip'),
self.define_from_variant('HDF5_ENABLE_SZIP_ENCODING', 'szip'),
self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
self.define('ONLY_SHARED_LIBS', False),
self.define_from_variant('HDF5_ENABLE_PARALLEL', 'mpi'),
self.define_from_variant('HDF5_ENABLE_THREADSAFE', 'threadsafe'),
self.define_from_variant('HDF5_BUILD_HL_LIB', 'hl'),
self.define_from_variant('HDF5_BUILD_CPP_LIB', 'cxx'),
self.define_from_variant('HDF5_BUILD_FORTRAN', 'fortran'),
self.define_from_variant('HDF5_BUILD_JAVA', 'java'),
self.define_from_variant('HDF5_BUILD_TOOLS', 'tools')
]
api = spec.variants['api'].value
if api != 'default':
args.append(self.define('DEFAULT_API_VERSION', api))
if '+mpi' in spec:
args.append(self.define('CMAKE_C_COMPILER', spec['mpi'].mpicc))
if '+cxx' in self.spec:
args.append(self.define('CMAKE_CXX_COMPILER',
spec['mpi'].mpicxx))
if '+fortran' in self.spec:
args.append(self.define('CMAKE_Fortran_COMPILER',
spec['mpi'].mpifc))
return args
@run_after('install')
def ensure_parallel_compiler_wrappers(self):
# When installed with Autotools and starting at least version 1.8.10,
# the package produces C compiler wrapper called either 'h5cc' (when MPI
# support is disabled) or 'h5pcc' (when MPI support is enabled). The
# CMake installation produces the wrapper called 'h5cc' (regardless of
# whether MPI support is enabled) only starting versions 1.8.21, 1.10.2
# and 1.12.0. The current develop versions also produce 'h5pcc' when MPI
# support is enabled and the file is identical to 'h5cc'. Here, we make
# sure that 'h5pcc' is available when MPI support is enabled (only for
# versions that generate 'h5cc').
if self.spec.satisfies('@1.8.21:1.8.22,1.10.2:1.10.7,1.12.0+mpi'):
with working_dir(self.prefix.bin):
# No try/except here, fix the condition above instead:
symlink('h5cc', 'h5pcc')
# The same as for 'h5pcc'. However, the CMake installation produces the
# Fortran compiler wrapper called 'h5fc' only starting versions 1.8.22,
# 1.10.6 and 1.12.0. The current develop versions do not produce 'h5pfc'
# at all. Here, we make sure that 'h5pfc' is available when Fortran and
# MPI support are enabled (only for versions that generate 'h5fc').
if self.spec.satisfies('@1.8.22:1.8,'
'1.10.6:1.10,'
'1.12.0:1.12,'
'develop:'
'+fortran+mpi'):
with working_dir(self.prefix.bin):
# No try/except here, fix the condition above instead:
symlink('h5fc', 'h5pfc')
@run_after('install')
def fix_package_config(self):
# We need to fix the pkg-config files, which are also used by the
# compiler wrappers. The files are created starting versions 1.8.21,
# 1.10.2 and 1.12.0. However, they are broken (except for the version
# 1.8.22): the files are named <name>-<version>.pc but reference <name>
# packages. This was fixed in the develop versions at some point: the
# files started referencing <name>-<version> packages but got broken
# again: the files got names <name>.pc but references had not been
# updated accordingly. Another issue, which we address here, is that
# some Linux distributions install pkg-config files named hdf5.pc and we
# want to override them. Therefore, the following solution makes sure
# that each <name>-<version>.pc file is symlinked by <name>.pc and all
# references to <name>-<version> packages in the original files are
# replaced with references to <name> packages.
pc_files = find(self.prefix.lib.pkgconfig, 'hdf5*.pc', recursive=False)
if not pc_files:
# This also tells us that the pkgconfig directory does not exist.
return
# Replace versioned references in all pkg-config files:
filter_file(
r'(Requires(?:\.private)?:.*)(hdf5[^\s,]*)(?:-[^\s,]*)(.*)',
r'\1\2\3', *pc_files, backup=False)
# Create non-versioned symlinks to the versioned pkg-config files:
with working_dir(self.prefix.lib.pkgconfig):
for f in pc_files:
src_filename = os.path.basename(f)
version_sep_idx = src_filename.find('-')
if version_sep_idx > -1:
tgt_filename = src_filename[:version_sep_idx] + '.pc'
if not os.path.exists(tgt_filename):
symlink(src_filename, tgt_filename)
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install(self):
self._check_install()
def _check_install(self):
# Build and run a small program to test the installed HDF5 library
spec = self.spec
print("Checking HDF5 installation...")
checkdir = "spack-check"
with working_dir(checkdir, create=True):
source = r"""
#include <hdf5.h>
#include <assert.h>
#include <stdio.h>
int main(int argc, char **argv) {
unsigned majnum, minnum, relnum;
herr_t herr = H5get_libversion(&majnum, &minnum, &relnum);
assert(!herr);
printf("HDF5 version %d.%d.%d %u.%u.%u\n", H5_VERS_MAJOR, H5_VERS_MINOR,
H5_VERS_RELEASE, majnum, minnum, relnum);
return 0;
}
"""
expected = """\
HDF5 version {version} {version}
""".format(version=str(spec.version.up_to(3)))
with open("check.c", 'w') as f:
f.write(source)
if '+mpi' in spec:
cc = Executable(spec['mpi'].mpicc)
else:
cc = Executable(self.compiler.cc)
cc(*(['-c', "check.c"] + spec['hdf5'].headers.cpp_flags.split()))
cc(*(['-o', "check",
"check.o"] + spec['hdf5'].libs.ld_flags.split()))
try:
check = Executable('./check')
output = check(output=str)
except ProcessError:
output = ""
success = output == expected
if not success:
print("Produced output does not match expected output.")
print("Expected output:")
print('-' * 80)
print(expected)
print('-' * 80)
print("Produced output:")
print('-' * 80)
print(output)
print('-' * 80)
raise RuntimeError("HDF5 install check failed")
shutil.rmtree(checkdir)
def _test_check_versions(self):
"""Perform version checks on selected installed package binaries."""
spec_vers_str = 'Version {0}'.format(self.spec.version)
exes = [
'h5copy', 'h5diff', 'h5dump', 'h5format_convert', 'h5ls',
'h5mkgrp', 'h5repack', 'h5stat', 'h5unjam',
]
use_short_opt = ['h52gif', 'h5repart', 'h5unjam']
for exe in exes:
reason = 'test: ensuring version of {0} is {1}' \
.format(exe, spec_vers_str)
option = '-V' if exe in use_short_opt else '--version'
self.run_test(exe, option, spec_vers_str, installed=True,
purpose=reason, skip_missing=True)
def _test_example(self):
"""This test performs copy, dump, and diff on an example hdf5 file."""
test_data_dir = self.test_suite.current_test_data_dir
filename = 'spack.h5'
h5_file = test_data_dir.join(filename)
reason = 'test: ensuring h5dump produces expected output'
expected = get_escaped_text_output(test_data_dir.join('dump.out'))
self.run_test('h5dump', filename, expected, installed=True,
purpose=reason, skip_missing=True,
work_dir=test_data_dir)
reason = 'test: ensuring h5copy runs'
options = ['-i', h5_file, '-s', 'Spack', '-o', 'test.h5', '-d',
'Spack']
self.run_test('h5copy', options, [], installed=True,
purpose=reason, skip_missing=True, work_dir='.')
reason = ('test: ensuring h5diff shows no differences between orig and'
' copy')
self.run_test('h5diff', [h5_file, 'test.h5'], [], installed=True,
purpose=reason, skip_missing=True, work_dir='.')
def test(self):
"""Perform smoke tests on the installed package."""
# Simple version check tests on known binaries
self._test_check_versions()
# Run sequence of commands on an hdf5 file
self._test_example()
# Run existing install check
self._check_install()
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