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{
lib,
fetchPypi,
fetchpatch,
buildPythonPackage,
pythonOlder,
setuptools,
numpy,
hdf5,
cython_0,
pkgconfig,
mpi4py ? null,
openssh,
pytestCheckHook,
pytest-mpi,
cached-property,
}:
assert hdf5.mpiSupport -> mpi4py != null && hdf5.mpi == mpi4py.mpi;
let
mpi = hdf5.mpi;
mpiSupport = hdf5.mpiSupport;
in
buildPythonPackage rec {
version = "3.11.0";
pname = "h5py";
pyproject = true;
disabled = pythonOlder "3.7";
src = fetchPypi {
inherit pname version;
hash = "sha256-e36PeAcqLt7IfJg28l80ID/UkqRHVwmhi0F6M8+yH6k=";
};
patches = [
# Unlock an overly strict locking of mpi4py version (seems not to be necessary).
# See also: https://github.com/h5py/h5py/pull/2418/files#r1589372479
./mpi4py-requirement.patch
# Fix 16-bit float dtype and tests on darwin (remove in next release)
(fetchpatch {
url = "https://github.com/h5py/h5py/commit/a27a1f49ce92d985e14b8a24fa80d30e5174add2.patch";
hash = "sha256-7TcmNSJucknq+Vnv4ViT6S0nWeH1+krarWxq6WXLYEA=";
})
];
# avoid strict pinning of numpy, can't be replaced with pythonRelaxDepsHook,
# see: https://github.com/NixOS/nixpkgs/issues/327941
postPatch = ''
substituteInPlace pyproject.toml \
--replace-fail "numpy >=2.0.0rc1" "numpy"
'';
pythonRelaxDeps = [ "mpi4py" ];
HDF5_DIR = "${hdf5}";
HDF5_MPI = if mpiSupport then "ON" else "OFF";
postConfigure = ''
# Needed to run the tests reliably. See:
# https://bitbucket.org/mpi4py/mpi4py/issues/87/multiple-test-errors-with-openmpi-30
${lib.optionalString mpiSupport "export OMPI_MCA_rmaps_base_oversubscribe=yes"}
'';
preBuild = lib.optionalString mpiSupport "export CC=${lib.getDev mpi}/bin/mpicc";
nativeBuildInputs = [
cython_0
pkgconfig
setuptools
];
buildInputs = [ hdf5 ] ++ lib.optional mpiSupport mpi;
propagatedBuildInputs =
[ numpy ]
++ lib.optionals mpiSupport [
mpi4py
openssh
]
++ lib.optionals (pythonOlder "3.8") [ cached-property ];
nativeCheckInputs = [
pytestCheckHook
pytest-mpi
openssh
];
# https://github.com/NixOS/nixpkgs/issues/255262
preCheck = ''
cd $out
'';
# For some reason these fail when mpi support is enabled, due to concurrent
# writings. There are a few open issues about this in the bug tracker, but
# not related to the tests.
disabledTests = lib.optionals mpiSupport [ "TestPageBuffering" ];
pythonImportsCheck = [ "h5py" ];
meta = {
changelog = "https://github.com/h5py/h5py/blob/${version}/docs/whatsnew/${lib.versions.majorMinor version}.rst";
description = "Pythonic interface to the HDF5 binary data format";
homepage = "http://www.h5py.org/";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ doronbehar ];
};
}
|
