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{
lib,
stdenv,
buildPythonPackage,
fetchPypi,
pythonOlder,
pythonRelaxDepsHook,
# python dependencies
click,
python-dateutil,
etelemetry,
filelock,
funcsigs,
future,
looseversion,
mock,
networkx,
nibabel,
numpy,
packaging,
prov,
psutil,
pybids,
pydot,
pytest,
pytest-xdist,
pytest-forked,
rdflib,
scipy,
simplejson,
traits,
xvfbwrapper,
codecov,
# 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,
}:
buildPythonPackage rec {
pname = "nipype";
version = "1.8.6";
disabled = pythonOlder "3.7";
format = "setuptools";
src = fetchPypi {
inherit pname version;
hash = "sha256-l3sTFej3D5QWPsB+MeVXG+g/Kt1gIxQcWgascAEm+NE=";
};
postPatch = ''
substituteInPlace nipype/interfaces/base/tests/test_core.py \
--replace "/usr/bin/env bash" "${bash}/bin/bash"
'';
nativeBuildInputs = [ pythonRelaxDepsHook ];
pythonRelaxDeps = [ "traits" ];
propagatedBuildInputs = [
click
python-dateutil
etelemetry
filelock
funcsigs
future
looseversion
networkx
nibabel
numpy
packaging
prov
psutil
pydot
rdflib
scipy
simplejson
traits
xvfbwrapper
];
nativeCheckInputs = [
pybids
codecov
glibcLocales
mock
pytest
pytest-forked
pytest-xdist
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 and not test_no_et_multiproc'
'';
pythonImportsCheck = [ "nipype" ];
meta = with lib; {
homepage = "https://nipy.org/nipype/";
description = "Neuroimaging in Python: Pipelines and Interfaces";
mainProgram = "nipypecli";
license = licenses.bsd3;
maintainers = with maintainers; [ ashgillman ];
};
}
|
