1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
|
{
lib,
fetchPypi,
buildPythonPackage,
pythonOlder,
setuptools,
numpy,
hdf5,
cython,
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 = "3.13.0";
pname = "h5py";
pyproject = true;
disabled = pythonOlder "3.7";
src = fetchPypi {
inherit pname version;
hash = "sha256-GHDkZRhyACPahdCJWhlg/yzjmMVnHqw7GkHsaWtxBcM=";
};
pythonRelaxDeps = [ "mpi4py" ];
# Avoid strict pinning of Numpy, can't be replaced with pythonRelaxDepsHook,
# as these are build time dependencies. See:
# https://github.com/NixOS/nixpkgs/issues/327941
postPatch = ''
substituteInPlace pyproject.toml \
--replace-fail "numpy >=2.0.0, <3" "numpy"
'';
env = {
HDF5_DIR = "${hdf5}";
HDF5_MPI = if mpiSupport then "ON" else "OFF";
# See discussion at https://github.com/h5py/h5py/issues/2560
H5PY_SETUP_REQUIRES = 0;
};
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";
build-system = [
cython
numpy
pkgconfig
setuptools
];
buildInputs = [ hdf5 ] ++ lib.optional mpiSupport mpi;
dependencies =
[ 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 ];
};
}
|
