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
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
|
{
lib,
stdenv,
fetchPypi,
fetchpatch,
buildPythonPackage,
blosc2,
bzip2,
c-blosc,
cython,
hdf5,
lzo,
numpy,
numexpr,
packaging,
pkg-config,
setuptools,
sphinx,
typing-extensions,
# Test inputs
python,
pytest,
py-cpuinfo,
}:
buildPythonPackage rec {
pname = "tables";
version = "3.10.2";
pyproject = true;
src = fetchPypi {
inherit pname version;
hash = "sha256-JUSBKnGG+tuoMdbdNOtJzNeI1qg/TkwrQxuDW2eWyRA=";
};
patches = [
# should be included in next release
(fetchpatch {
name = "numexpr-2.13.0-compat.patch";
url = "https://github.com/PyTables/PyTables/commit/41270019ce1ffd97ce8f23b21d635e00e12b0ccb.patch";
hash = "sha256-CaDBYKiABVtlM5e9ChCsf8dWOwEnMPOIXQ100JTnlnE=";
})
];
build-system = [
blosc2
cython
setuptools
sphinx
];
nativeBuildInputs = [
pkg-config
];
buildInputs = [
bzip2
c-blosc
blosc2.c-blosc2
hdf5
lzo
];
dependencies = [
blosc2
py-cpuinfo
numpy
numexpr
packaging # uses packaging.version at runtime
typing-extensions
];
# When doing `make distclean`, ignore docs
postPatch = ''
# Force test suite to error when unittest runner fails
substituteInPlace tables/tests/test_suite.py \
--replace-fail "return 0" "assert result.wasSuccessful(); return 0" \
--replace-fail "return 1" "assert result.wasSuccessful(); return 1"
substituteInPlace tables/__init__.py \
--replace-fail 'find_library("blosc2")' '"${lib.getLib c-blosc}/lib/libblosc${stdenv.hostPlatform.extensions.sharedLibrary}"' '';
env = {
HDF5_DIR = lib.getDev hdf5;
};
# Regenerate C code with Cython
preBuild = ''
make distclean
'';
pypaBuildFlags = [
"--config-setting=--build-option=--hdf5=${lib.getDev hdf5}"
"--config-setting=--build-option=--lzo=${lib.getDev lzo}"
"--config-setting=--build-option=--bzip2=${lib.getDev bzip2}"
"--config-setting=--build-option=--blosc=${lib.getDev c-blosc}"
"--config-setting=--build-option=--blosc2=${lib.getDev blosc2.c-blosc2}"
];
nativeCheckInputs = [ pytest ];
preCheck = ''
export HOME=$(mktemp -d)
cd ..
'';
# Runs the light (yet comprehensive) subset of the test suite.
# The whole "heavy" test suite supposedly takes ~4 hours to run.
checkPhase = ''
runHook preCheck
${python.interpreter} -m tables.tests.test_all
runHook postCheck
'';
pythonImportsCheck = [ "tables" ];
meta = {
description = "Hierarchical datasets for Python";
homepage = "https://www.pytables.org/";
changelog = "https://github.com/PyTables/PyTables/releases/tag/v${version}";
license = lib.licenses.bsd2;
maintainers = [ ];
};
}
|
