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Merge pull request #228171 from bcdarwin/unbreak-pybids-nipype-heudiconv

python310Packages.nipype: unbreak

authored by

Weijia Wang and committed by
GitHub 5f93ecea b4ed0a1f

+36 -58
unified split
+12 -15
pkgs/development/python-modules/nipype/default.nix
··· 1 1 { lib, stdenv 2 2 , buildPythonPackage 3 3 , fetchPypi 4 - , isPy27 4 + , pythonOlder 5 + , pythonRelaxDepsHook 5 6 # python dependencies 6 7 , click 7 8 , python-dateutil ··· 9 10 , filelock 10 11 , funcsigs 11 12 , future 13 + , looseversion 12 14 , mock 13 15 , networkx 14 16 , nibabel ··· 26 28 , simplejson 27 29 , traits 28 30 , xvfbwrapper 29 - , pytest-cov 30 31 , codecov 31 - , sphinx 32 32 # other dependencies 33 33 , which 34 34 , bash ··· 40 40 , useNeurdflib ? false 41 41 }: 42 42 43 - let 44 - 45 - # This is a temporary convenience package for changes waiting to be merged into the primary rdflib repo. 46 - neurdflib = callPackage ./neurdflib.nix { }; 47 - 48 - in 49 - 50 43 buildPythonPackage rec { 51 44 pname = "nipype"; 52 45 version = "1.8.5"; 53 - disabled = isPy27; 46 + disabled = pythonOlder "3.7"; 47 + format = "setuptools"; 54 48 55 49 src = fetchPypi { 56 50 inherit pname version; ··· 63 57 ''; 64 58 65 59 nativeBuildInputs = [ 66 - sphinx 60 + pythonRelaxDepsHook 67 61 ]; 68 62 63 + pythonRelaxDeps = [ "traits" ]; 64 + 69 65 propagatedBuildInputs = [ 70 66 click 71 67 python-dateutil ··· 73 69 filelock 74 70 funcsigs 75 71 future 72 + looseversion 76 73 networkx 77 74 nibabel 78 75 numpy ··· 80 77 prov 81 78 psutil 82 79 pydot 80 + rdflib 83 81 scipy 84 82 simplejson 85 83 traits 86 84 xvfbwrapper 87 - ] ++ [ (if useNeurdflib then neurdflib else rdflib) ]; 85 + ]; 88 86 89 87 nativeCheckInputs = [ 90 88 pybids ··· 94 92 pytest 95 93 pytest-forked 96 94 pytest-xdist 97 - pytest-cov 98 95 which 99 96 ]; 100 97 ··· 102 99 doCheck = !stdenv.isDarwin; 103 100 # ignore tests which incorrect fail to detect xvfb 104 101 checkPhase = '' 105 - LC_ALL="en_US.UTF-8" pytest nipype/tests -k 'not display' 102 + LC_ALL="en_US.UTF-8" pytest nipype/tests -k 'not display and not test_no_et_multiproc' 106 103 ''; 107 104 pythonImportsCheck = [ "nipype" ]; 108 105
-38
pkgs/development/python-modules/nipype/neurdflib.nix
··· 1 - { lib 2 - , buildPythonPackage 3 - , fetchPypi 4 - , isodate 5 - , html5lib 6 - , sparqlwrapper 7 - , networkx 8 - , nose 9 - , python 10 - }: 11 - 12 - buildPythonPackage rec { 13 - pname = "neurdflib"; 14 - version = "5.0.1"; 15 - 16 - src = fetchPypi { 17 - inherit pname version; 18 - sha256 = "d34493cee15029ff5db16157429585ff863ba5542675a4d8a94a0da1bc6e3a50"; 19 - }; 20 - 21 - propagatedBuildInputs = [ isodate html5lib sparqlwrapper ]; 22 - 23 - nativeCheckInputs = [ networkx nose ]; 24 - 25 - # Python 2 syntax 26 - # Failing doctest 27 - doCheck = false; 28 - 29 - checkPhase = '' 30 - ${python.interpreter} run_tests.py 31 - ''; 32 - 33 - meta = with lib; { 34 - description = "A temporary convenience package for changes waiting to be merged into the primary rdflib repo"; 35 - homepage = "https://pypi.org/project/neurdflib"; 36 - license = licenses.bsd3; 37 - }; 38 - }
+24 -5
pkgs/development/python-modules/pybids/default.nix
··· 1 1 { buildPythonPackage 2 2 , lib 3 3 , fetchPypi 4 + , fetchpatch 5 + , formulaic 4 6 , click 5 7 , num2words 6 8 , numpy ··· 11 13 , bids-validator 12 14 , sqlalchemy 13 15 , pytestCheckHook 16 + , versioneer 17 + , pythonRelaxDepsHook 14 18 }: 15 19 16 20 buildPythonPackage rec { 17 - version = "0.15.5"; 21 + version = "0.15.6"; 18 22 pname = "pybids"; 19 23 20 24 src = fetchPypi { 21 25 inherit pname version; 22 - hash = "sha256-ryIiWpFoh0KSmyLI4LDn+EkXEYwDIr8/A7opoZJ+bo4="; 26 + hash = "sha256-OjWW08tyVDHkF0X3Pa+10HYD/7Gysp5DkEt9LaVxsdM="; 23 27 }; 24 28 29 + patches = [ 30 + # remove after next release 31 + (fetchpatch { 32 + name = "fix-pybids-sqlalchemy-dep"; 33 + url = "https://github.com/bids-standard/pybids/commit/5f008dfc282394ef94a68d47dba37ceead9eac9a.patch"; 34 + hash = "sha256-gx6w35XqDBZ8cTGHeY/mz2xNQqza9E5z8bRJR7mbPcg="; 35 + excludes = [ "pyproject.toml" ]; # not in PyPI dist 36 + }) 37 + ]; 38 + 39 + nativeBuildInputs = [ pythonRelaxDepsHook ]; 40 + 41 + pythonRelaxDeps = [ "sqlalchemy" ]; 42 + 25 43 propagatedBuildInputs = [ 26 44 click 45 + formulaic 27 46 num2words 28 47 numpy 29 48 scipy ··· 32 51 patsy 33 52 bids-validator 34 53 sqlalchemy 54 + versioneer 35 55 ]; 36 56 37 57 nativeCheckInputs = [ pytestCheckHook ]; 38 58 pythonImportsCheck = [ "bids" ]; 59 + # looks for missing data: 60 + disabledTests = [ "test_config_filename" ]; 39 61 40 62 meta = with lib; { 41 63 description = "Python tools for querying and manipulating BIDS datasets"; 42 64 homepage = "https://github.com/bids-standard/pybids"; 43 65 license = licenses.mit; 44 66 maintainers = with maintainers; [ jonringer ]; 45 - # Doesn't support sqlalchemy >=1.4 46 - # See https://github.com/bids-standard/pybids/issues/680 47 - broken = true; 48 67 }; 49 68 }