{ stdenv
, buildPythonPackage
, fetchPypi
, isPy3k
, isPy38
# python dependencies
, click
, configparser ? null
, dateutil
, etelemetry
, filelock
, funcsigs
, future
, futures
, mock
, networkx
, nibabel
, numpy
, packaging
, pathlib2
, prov
, psutil
, pybids
, pydot
, pytest
, pytest_xdist
, pytest-forked
, scipy
, simplejson
, traits
, xvfbwrapper
, pytestcov
, codecov
# other dependencies
, which
, bash
, glibcLocales
, callPackage
}:
assert !isPy3k -> configparser != null;
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 = "1.3.1";
src = fetchPypi {
inherit pname version;
sha256 = "bb190964b568d64b04b73d2aa7eae31061fdbc3051d8c27bb34b1632db07ec71";
};
postPatch = ''
substituteInPlace nipype/interfaces/base/tests/test_core.py \
--replace "/usr/bin/env bash" "${bash}/bin/bash"
'';
propagatedBuildInputs = [
click
dateutil
etelemetry
filelock
funcsigs
future
networkx
neurdflib
nibabel
numpy
packaging
prov
psutil
pydot
scipy
simplejson
traits
xvfbwrapper
] ++ stdenv.lib.optionals (!isPy3k) [
configparser
futures
pathlib2 # darwin doesn't receive this transitively, but it is in install_requires
];
checkInputs = [
pybids
codecov
glibcLocales
mock
pytest
pytest-forked
pytest_xdist
pytestcov
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 -v nipype -k 'not display'
'';
meta = with stdenv.lib; {
homepage = "https://nipy.org/nipype/";
description = "Neuroimaging in Python: Pipelines and Interfaces";
license = licenses.bsd3;
maintainers = with maintainers; [ ashgillman ];
# tests hang, blocking reviews of other packages
broken = isPy38;
};
}