pyrox.dev
Merge pull request #308478 from natsukium/htseq/update
python311Packages.htseq: 0.12.4 -> 2.0.4
authored by OTABI Tomoya and committed by GitHub 0204bbde be9b31b7
+61
-11
pkgs/development/python-modules/htseq/default.nix
+61
-11
pkgs/development/python-modules/htseq/default.nix
···
1
-
{ lib, buildPythonPackage, fetchFromGitHub, cython, numpy, pysam, matplotlib, python, isPy27, isPy3k }:
1
+
{
2
+
lib,
3
+
buildPythonPackage,
4
+
fetchFromGitHub,
5
+
fetchpatch,
6
+
swig,
7
+
cython,
8
+
matplotlib,
9
+
numpy,
10
+
pandas,
11
+
pysam,
12
+
setuptools,
13
+
pytestCheckHook,
14
+
nix-update-script,
15
+
}:
2
16
buildPythonPackage rec {
3
-
version = "0.12.4";
4
-
format = "setuptools";
5
17
pname = "htseq";
18
+
version = "2.0.4";
19
+
pyproject = true;
6
20
7
21
src = fetchFromGitHub {
8
22
owner = "htseq";
9
23
repo = "htseq";
10
24
rev = "release_${version}";
11
-
sha256 = "0y7vh249sljqjnv81060w4xkdx6f1y5zdqkh38yk926x6v9riijm";
25
+
hash = "sha256-7ocrmuj9LOtPz9XbI5rKGcdE5JbFz/pZh00Nie65XxE=";
12
26
};
13
27
14
-
nativeBuildInputs = [ cython ];
15
-
propagatedBuildInputs = [ numpy pysam matplotlib ];
28
+
patches = [
29
+
# https://github.com/htseq/htseq/pull/84
30
+
(fetchpatch {
31
+
name = "replace-distutils-with-sysconfig.patch";
32
+
url = "https://github.com/htseq/htseq/commit/f0f1e464ee9aee56f0b44f905e7b3355b0bb8f29.patch";
33
+
hash = "sha256-yDYkXCPy+YFgnk1rnXwCB998aZwVd5nJeejZIgeEzAo=";
34
+
})
35
+
];
16
36
17
-
checkPhase = lib.optionalString isPy27 ''
18
-
${python.interpreter} python2/test/test_general.py
19
-
'' + lib.optionalString isPy3k ''
20
-
${python.interpreter} python3/test/test_general.py
37
+
nativeBuildInputs = [ swig ];
38
+
39
+
build-system = [
40
+
cython
41
+
numpy
42
+
pysam
43
+
setuptools
44
+
];
45
+
46
+
dependencies = [
47
+
numpy
48
+
pysam
49
+
];
50
+
51
+
optional-dependencies = {
52
+
htseq-qa = [ matplotlib ];
53
+
};
54
+
55
+
pythonImportsCheck = [ "HTSeq" ];
56
+
57
+
nativeCheckInputs = [
58
+
pandas
59
+
pytestCheckHook
60
+
] ++ optional-dependencies.htseq-qa;
61
+
62
+
preCheck = ''
63
+
rm -r src HTSeq
64
+
export PATH=$out/bin:$PATH
21
65
'';
22
66
67
+
passthru.updateScript = nix-update-script {
68
+
extraArgs = [
69
+
"--version-regex"
70
+
"release_(.+)"
71
+
];
72
+
};
73
+
23
74
meta = with lib; {
24
75
homepage = "https://htseq.readthedocs.io/";
25
76
description = "A framework to work with high-throughput sequencing data";
26
77
maintainers = with maintainers; [ unode ];
27
-
platforms = platforms.unix;
28
78
};
29
79
}