nixpkgs/pkgs/development/python-modules/nipype/default.nix
Profpatsch 4a7f99d55d treewide: with stdenv.lib; in meta -> with lib;
Part of: https://github.com/NixOS/nixpkgs/issues/108938

meta = with stdenv.lib;

is a widely used pattern. We want to slowly remove
the `stdenv.lib` indirection and encourage people
to use `lib` directly. Thus let’s start with the meta
field.

This used a rewriting script to mostly automatically
replace all occurances of this pattern, and add the
`lib` argument to the package header if it doesn’t
exist yet.

The script in its current form is available at
https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix
2021-01-11 10:38:22 +01:00

116 lines
2.1 KiB
Nix

{ lib, stdenv
, buildPythonPackage
, fetchPypi
, isPy27
# python dependencies
, click
, dateutil
, etelemetry
, filelock
, funcsigs
, future
, mock
, networkx
, nibabel
, numpy
, packaging
, prov
, psutil
, pybids
, pydot
, pytest
, pytest_xdist
, pytest-forked
, rdflib
, scipy
, simplejson
, traits
, xvfbwrapper
, pytestcov
, 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 = "1.6.0";
disabled = isPy27;
src = fetchPypi {
inherit pname version;
sha256 = "bc56ce63f74c9a9a23c6edeaf77631377e8ad2bea928c898cc89527a47f101cf";
};
postPatch = ''
substituteInPlace nipype/interfaces/base/tests/test_core.py \
--replace "/usr/bin/env bash" "${bash}/bin/bash"
'';
nativeBuildInputs = [
sphinx
];
propagatedBuildInputs = [
click
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
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 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 ];
};
}