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115 lines
2.1 KiB
115 lines
2.1 KiB
{ lib, stdenv
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, buildPythonPackage
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, fetchPypi
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, isPy27
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# python dependencies
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, click
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, python-dateutil
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, etelemetry
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, filelock
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, funcsigs
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, future
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, mock
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, networkx
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, nibabel
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, numpy
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, packaging
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, prov
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, psutil
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, pybids
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, pydot
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, pytest
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, pytest-xdist
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, pytest-forked
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, rdflib
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, scipy
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, simplejson
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, traits
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, xvfbwrapper
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, pytest-cov
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, codecov
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, sphinx
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# other dependencies
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, which
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, bash
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, glibcLocales
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, callPackage
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# causes Python packaging conflict with any package requiring rdflib,
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# so use the unpatched rdflib by default (disables Nipype provenance tracking);
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# see https://github.com/nipy/nipype/issues/2888:
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, useNeurdflib ? false
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}:
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let
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# This is a temporary convenience package for changes waiting to be merged into the primary rdflib repo.
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neurdflib = callPackage ./neurdflib.nix { };
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in
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buildPythonPackage rec {
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pname = "nipype";
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version = "1.7.0";
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disabled = isPy27;
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src = fetchPypi {
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inherit pname version;
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sha256 = "e689fe2e5049598c9cd3708e8df1cac732fa1a88696f283e3bc0a70fecb8ab51";
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};
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postPatch = ''
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substituteInPlace nipype/interfaces/base/tests/test_core.py \
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--replace "/usr/bin/env bash" "${bash}/bin/bash"
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'';
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nativeBuildInputs = [
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sphinx
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];
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propagatedBuildInputs = [
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click
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python-dateutil
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etelemetry
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filelock
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funcsigs
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future
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networkx
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nibabel
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numpy
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packaging
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prov
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psutil
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pydot
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scipy
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simplejson
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traits
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xvfbwrapper
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] ++ [ (if useNeurdflib then neurdflib else rdflib) ];
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checkInputs = [
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pybids
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codecov
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glibcLocales
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mock
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pytest
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pytest-forked
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pytest-xdist
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pytest-cov
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which
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];
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# checks on darwin inspect memory which doesn't work in build environment
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doCheck = !stdenv.isDarwin;
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# ignore tests which incorrect fail to detect xvfb
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checkPhase = ''
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LC_ALL="en_US.UTF-8" pytest nipype/tests -k 'not display'
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'';
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pythonImportsCheck = [ "nipype" ];
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meta = with lib; {
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homepage = "https://nipy.org/nipype/";
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description = "Neuroimaging in Python: Pipelines and Interfaces";
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license = licenses.bsd3;
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maintainers = with maintainers; [ ashgillman ];
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};
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}
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