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{ 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 = "1.6.1";
disabled = isPy27;
src = fetchPypi {
inherit pname version;
sha256 = "8428cfc633d8e3b8c5650e241e9eedcf637b7969bcd40f3423334d4c6b0992b5";
};
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 ];
};
}
|