pyrox.dev
1{ lib, stdenv
2, buildPythonPackage
3, fetchPypi
4, isPy27
5# python dependencies
6, click
7, python-dateutil
8, etelemetry
9, filelock
10, funcsigs
11, future
12, mock
13, networkx
14, nibabel
15, numpy
16, packaging
17, prov
18, psutil
19, pybids
20, pydot
21, pytest
22, pytest-xdist
23, pytest-forked
24, rdflib
25, scipy
26, simplejson
27, traits
28, xvfbwrapper
29, pytest-cov
30, codecov
31, sphinx
32# other dependencies
33, which
34, bash
35, glibcLocales
36, callPackage
37# causes Python packaging conflict with any package requiring rdflib,
38# so use the unpatched rdflib by default (disables Nipype provenance tracking);
39# see https://github.com/nipy/nipype/issues/2888:
40, useNeurdflib ? false
41}:
42
43let
44
45 # This is a temporary convenience package for changes waiting to be merged into the primary rdflib repo.
46 neurdflib = callPackage ./neurdflib.nix { };
47
48in
49
50buildPythonPackage rec {
51 pname = "nipype";
52 version = "1.8.4";
53 disabled = isPy27;
54
55 src = fetchPypi {
56 inherit pname version;
57 sha256 = "sha256-yoG6iLfF7ugBL4eNC9OLINIzBj1YgF4TVngFKb77qak=";
58 };
59
60 postPatch = ''
61 substituteInPlace nipype/interfaces/base/tests/test_core.py \
62 --replace "/usr/bin/env bash" "${bash}/bin/bash"
63 '';
64
65 nativeBuildInputs = [
66 sphinx
67 ];
68
69 propagatedBuildInputs = [
70 click
71 python-dateutil
72 etelemetry
73 filelock
74 funcsigs
75 future
76 networkx
77 nibabel
78 numpy
79 packaging
80 prov
81 psutil
82 pydot
83 scipy
84 simplejson
85 traits
86 xvfbwrapper
87 ] ++ [ (if useNeurdflib then neurdflib else rdflib) ];
88
89 checkInputs = [
90 pybids
91 codecov
92 glibcLocales
93 mock
94 pytest
95 pytest-forked
96 pytest-xdist
97 pytest-cov
98 which
99 ];
100
101 # checks on darwin inspect memory which doesn't work in build environment
102 doCheck = !stdenv.isDarwin;
103 # ignore tests which incorrect fail to detect xvfb
104 checkPhase = ''
105 LC_ALL="en_US.UTF-8" pytest nipype/tests -k 'not display'
106 '';
107 pythonImportsCheck = [ "nipype" ];
108
109 meta = with lib; {
110 homepage = "https://nipy.org/nipype/";
111 description = "Neuroimaging in Python: Pipelines and Interfaces";
112 license = licenses.bsd3;
113 maintainers = with maintainers; [ ashgillman ];
114 };
115}