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
|
{ lib, stdenv
, buildPythonPackage
, fetchPypi
, isPy27
# python dependencies
, click
, python-dateutil
, etelemetry
, filelock
, funcsigs
, future
, mock
, networkx
, nibabel
, numpy
, packaging
, prov
, psutil
, pybids
, pydot
, pytest
, pytest-xdist
, pytest-forked
, rdflib
, scipy
, simplejson
, traits
, xvfbwrapper
, pytest-cov
, codecov
, sphinx
# other dependencies
, which
, bash
, glibcLocales
, callPackage
# causes Python packaging conflict with any package requiring rdflib,
# so use the unpatched rdflib by default (disables Nipype provenance tracking);
# see https://github.com/nipy/nipype/issues/2888:
, useNeurdflib ? false
}:
let
# This is a temporary convenience package for changes waiting to be merged into the primary rdflib repo.
neurdflib = callPackage ./neurdflib.nix { };
in
buildPythonPackage rec {
pname = "nipype";
version = "1.8.3";
disabled = isPy27;
src = fetchPypi {
inherit pname version;
sha256 = "sha256-Z/qa0NotxWFzweFHRm/MbJImivV8AZl68yiQ1jNvcAQ=";
};
postPatch = ''
substituteInPlace nipype/interfaces/base/tests/test_core.py \
--replace "/usr/bin/env bash" "${bash}/bin/bash"
'';
nativeBuildInputs = [
sphinx
];
propagatedBuildInputs = [
click
python-dateutil
etelemetry
filelock
funcsigs
future
networkx
nibabel
numpy
packaging
prov
psutil
pydot
scipy
simplejson
traits
xvfbwrapper
] ++ [ (if useNeurdflib then neurdflib else rdflib) ];
checkInputs = [
pybids
codecov
glibcLocales
mock
pytest
pytest-forked
pytest-xdist
pytest-cov
which
];
# checks on darwin inspect memory which doesn't work in build environment
doCheck = !stdenv.isDarwin;
# ignore tests which incorrect fail to detect xvfb
checkPhase = ''
LC_ALL="en_US.UTF-8" pytest nipype/tests -k 'not display'
'';
pythonImportsCheck = [ "nipype" ];
meta = with lib; {
homepage = "https://nipy.org/nipype/";
description = "Neuroimaging in Python: Pipelines and Interfaces";
license = licenses.bsd3;
maintainers = with maintainers; [ ashgillman ];
};
}
|