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
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
|
{
lib,
stdenv,
fetchurl,
writeText,
python,
buildPythonPackage,
fetchFromGitHub,
fetchpatch,
# build-system
cython,
gfortran,
meson-python,
nukeReferences,
pythran,
pkg-config,
setuptools,
xcbuild,
# buildInputs
# Upstream has support for using Darwin's Accelerate package. However this
# requires a Darwin user to work on a nice way to do that via an override.
# See:
# https://github.com/scipy/scipy/blob/v1.14.0/scipy/meson.build#L194-L211
blas,
lapack,
pybind11,
pooch,
xsimd,
# dependencies
numpy,
# tests
hypothesis,
pytest7CheckHook,
pytest-xdist,
# Reverse dependency
sage,
}:
let
pname = "scipy";
# DON'T UPDATE THESE ATTRIBUTES MANUALLY - USE:
#
# nix-shell maintainers/scripts/update.nix --argstr package python3.pkgs.scipy
#
# The update script uses sed regexes to replace them with the updated hashes.
version = "1.14.0";
srcHash = "sha256-rNplvbDExmMfcPuvhs+y9j5/9G6QR1GdMgQLty6oi2c=";
datasetsHashes = {
ascent = "1qjp35ncrniq9rhzb14icwwykqg2208hcssznn3hz27w39615kh3";
ecg = "1bwbjp43b7znnwha5hv6wiz3g0bhwrpqpi75s12zidxrbwvd62pj";
face = "11i8x29h80y7hhyqhil1fg8mxag5f827g33lhnsf44qk116hp2wx";
};
datasets = lib.mapAttrs (
d: hash:
fetchurl {
url = "https://raw.githubusercontent.com/scipy/dataset-${d}/main/${d}.dat";
sha256 = hash;
}
) datasetsHashes;
# Additional cross compilation related properties that scipy reads in scipy/meson.build
crossFileScipy = writeText "cross-file-scipy.conf" ''
[properties]
numpy-include-dir = '${numpy.coreIncludeDir}'
pythran-include-dir = '${pythran}/${python.sitePackages}/pythran'
host-python-path = '${python.interpreter}'
host-python-version = '${python.pythonVersion}'
'';
in
buildPythonPackage {
inherit pname version;
pyproject = true;
src = fetchFromGitHub {
owner = "scipy";
repo = "scipy";
rev = "refs/tags/v${version}";
hash = srcHash;
fetchSubmodules = true;
};
patches = [
# Helps with cross compilation, see https://github.com/scipy/scipy/pull/18167
(fetchpatch {
url = "https://github.com/scipy/scipy/commit/dd50ac9d98dbb70625333a23e3a90e493228e3be.patch";
hash = "sha256-Vf6/hhwu6X5s8KWhq8bUZKtSkdVu/GtEpGtj8Olxe7s=";
excludes = [ "doc/source/dev/contributor/meson_advanced.rst" ];
})
];
# Upstream says in a comment in their pyproject.toml that building against
# both numpy 2 and numpy 1 should work, but they seem to worry about numpy
# incompatibilities that we here with Nixpkgs' Python ecosystem, shouldn't
# experience.
postPatch = ''
substituteInPlace pyproject.toml \
--replace-fail 'numpy>=2.0.0rc1,' 'numpy' \
--replace-fail "pybind11>=2.12.0,<2.13.0" "pybind11>=2.12.0" \
'';
build-system =
[
cython
gfortran
meson-python
nukeReferences
pythran
pkg-config
setuptools
]
++ lib.optionals stdenv.hostPlatform.isDarwin [
# Minimal version required according to:
# https://github.com/scipy/scipy/blob/v1.14.0/scipy/meson.build#L185-L188
(xcbuild.override {
sdkVer = "13.3";
})
];
buildInputs = [
blas
lapack
pybind11
pooch
xsimd
];
dependencies = [ numpy ];
__darwinAllowLocalNetworking = true;
nativeCheckInputs = [
hypothesis
# Failed: DID NOT WARN. No warnings of type (<class 'DeprecationWarning'>, <class 'PendingDeprecationWarning'>, <class 'FutureWarning'>) were emitted.
pytest7CheckHook
pytest-xdist
];
# The following tests are broken on aarch64-darwin with newer compilers and library versions.
# See https://github.com/scipy/scipy/issues/18308
disabledTests = lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
"test_a_b_neg_int_after_euler_hypergeometric_transformation"
"test_dst4_definition_ortho"
"test_load_mat4_le"
"hyp2f1_test_case47"
"hyp2f1_test_case3"
"test_uint64_max"
];
doCheck = !(stdenv.hostPlatform.isx86_64 && stdenv.hostPlatform.isDarwin);
preConfigure =
''
# Helps parallelization a bit
export NPY_NUM_BUILD_JOBS=$NIX_BUILD_CORES
# We download manually the datasets and this variable tells the pooch
# library where these files are cached. See also:
# https://github.com/scipy/scipy/pull/18518#issuecomment-1562350648 And at:
# https://github.com/scipy/scipy/pull/17965#issuecomment-1560759962
export XDG_CACHE_HOME=$PWD; export HOME=$(mktemp -d); mkdir scipy-data
''
+ (lib.concatStringsSep "\n" (
lib.mapAttrsToList (
d: dpath:
# Actually copy the datasets
"cp ${dpath} scipy-data/${d}.dat"
) datasets
));
mesonFlags = [
"-Dblas=${blas.pname}"
"-Dlapack=${lapack.pname}"
# We always run what's necessary for cross compilation, which is passing to
# meson the proper cross compilation related arguments. See also:
# https://docs.scipy.org/doc/scipy/building/cross_compilation.html
"--cross-file=${crossFileScipy}"
];
# disable stackprotector on aarch64-darwin for now
#
# build error:
#
# /private/tmp/nix-build-python3.9-scipy-1.6.3.drv-0/ccDEsw5U.s:109:15: error: index must be an integer in range [-256, 255].
#
# ldr x0, [x0, ___stack_chk_guard];momd
#
hardeningDisable = lib.optionals (stdenv.hostPlatform.isAarch64 && stdenv.hostPlatform.isDarwin) [
"stackprotector"
];
# remove references to dev dependencies
postInstall = ''
nuke-refs $out/${python.sitePackages}/scipy/__config__.py
rm $out/${python.sitePackages}/scipy/__pycache__/__config__.*.opt-1.pyc
'';
preCheck = ''
export OMP_NUM_THREADS=$(( $NIX_BUILD_CORES / 4 ))
cd $out
'';
requiredSystemFeatures = [ "big-parallel" ]; # the tests need lots of CPU time
passthru = {
inherit blas;
updateScript =
[
./update.sh
# Pass it this file name as argument
(builtins.unsafeGetAttrPos "pname" python.pkgs.scipy).file
]
# Pass it the names of the datasets to update their hashes
++ (builtins.attrNames datasetsHashes);
tests = {
inherit sage;
};
};
SCIPY_USE_G77_ABI_WRAPPER = 1;
meta = {
changelog = "https://github.com/scipy/scipy/releases/tag/v${version}";
description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering";
downloadPage = "https://github.com/scipy/scipy";
homepage = "https://www.scipy.org/";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ doronbehar ];
};
}
|
