Unverified Commit 0142706e authored by Weijia Wang's avatar Weijia Wang Committed by GitHub
Browse files

Merge pull request #312707 from fabaff/pybids-fix 

python312Packages.pybids: disable failing tests
parents e18afd63 3dbac594

pkgs/development/python-modules/dcmstack/default.nix

+24 −12
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, pythonOlder

, pytestCheckHook

, nibabel

, pydicom

, pylibjpeg-libjpeg

{

  lib,

  buildPythonPackage,

  fetchFromGitHub,

  nibabel,

  pydicom,

  pylibjpeg-libjpeg,

  pytestCheckHook,

  pythonOlder,

  setuptools,

}:



buildPythonPackage rec {

  pname = "dcmstack";

  version = "0.9";

  format = "setuptools";

  pyproject = true;



  disabled = pythonOlder "3.7";



  src = fetchFromGitHub {

    owner = "moloney";

    repo = pname;

    repo = "dcmstack";

    rev = "refs/tags/v${version}";

    hash = "sha256-GVzih9H2m2ZGSuZMRuaDG78b95PI3j0WQw5M3l4KNCs=";

  };



  propagatedBuildInputs = [

  build-system = [ setuptools ];



  dependencies = [

    nibabel

    pydicom

    pylibjpeg-libjpeg
@@ -29,9 +34,16 @@ buildPythonPackage rec { 


  nativeCheckInputs = [ pytestCheckHook ];



  pythonImportsCheck = [ "dcmstack" ];



  disabledTestPaths = [

    # AttributeError: 'TestNitoolCli' object has no attribute 'out_dir'

    "test/test_cli.py"

  ];



  meta = with lib; {

    homepage = "https://github.com/moloney/dcmstack";

    description = "DICOM to Nifti conversion preserving metadata";

    homepage = "https://github.com/moloney/dcmstack";

    license = licenses.mit;

    maintainers = with maintainers; [ bcdarwin ];

  };

pkgs/development/python-modules/heudiconv/default.nix

+30 −28
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, datalad

, dcm2niix

, dcmstack

, etelemetry

, fetchPypi

, filelock

, git

, nibabel

, nipype

, pydicom

, pytestCheckHook

, pythonOlder

, setuptools

, versioningit

, wheel

{

  lib,

  buildPythonPackage,

  datalad,

  dcm2niix,

  dcmstack,

  etelemetry,

  fetchPypi,

  filelock,

  git,

  nibabel,

  nipype,

  pydicom,

  pytestCheckHook,

  pythonOlder,

  setuptools,

  versioningit,

}:



buildPythonPackage rec {

  pname = "heudiconv";

  version = "1.1.0";

  format = "pyproject";

  pyproject = true;



  disabled = pythonOlder "3.8";
@@ -31,22 +31,21 @@ buildPythonPackage rec { 


  postPatch = ''

    substituteInPlace pyproject.toml \

      --replace "versioningit ~=" "versioningit >="

      --replace-fail "versioningit ~=" "versioningit >="

  '';



  nativeBuildInputs = [

  build-system = [

    setuptools

    versioningit

    wheel

  ];



  propagatedBuildInputs = [

    nibabel

    pydicom

    nipype

  dependencies = [

    dcmstack

    etelemetry

    filelock

    nibabel

    nipype

    pydicom

  ];



  nativeCheckInputs = [
@@ -60,13 +59,16 @@ buildPythonPackage rec { 
    export HOME=$(mktemp -d)

  '';



  pythonImportsCheck = [

    "heudiconv"

  pythonImportsCheck = [ "heudiconv" ];



  disabledTests = [

    # No such file or directory

    "test_bvals_are_zero"

  ];



  meta = with lib; {

    homepage = "https://heudiconv.readthedocs.io";

    description = "Flexible DICOM converter for organizing imaging data";

    homepage = "https://heudiconv.readthedocs.io";

    changelog = "https://github.com/nipy/heudiconv/releases/tag/v${version}";

    license = licenses.asl20;

    maintainers = with maintainers; [ bcdarwin ];

pkgs/development/python-modules/pybids/default.nix

+26 −25
Original line number Diff line number Diff line 
{ buildPythonPackage

, lib

, fetchPypi

, setuptools

, formulaic

, click

, num2words

, numpy

, scipy

, pandas

, nibabel

, bids-validator

, sqlalchemy

, pytestCheckHook

, versioneer

, pythonRelaxDepsHook

{

  lib,

  buildPythonPackage,

  fetchPypi,

  setuptools,

  formulaic,

  click,

  num2words,

  numpy,

  scipy,

  pandas,

  nibabel,

  bids-validator,

  sqlalchemy,

  pytestCheckHook,

  versioneer,

  pythonRelaxDepsHook,

}:



buildPythonPackage rec {
@@ -49,28 +50,28 @@ buildPythonPackage rec { 
    sqlalchemy

  ];



  pythonImportsCheck = [

    "bids"

  ];

  pythonImportsCheck = [ "bids" ];



  nativeCheckInputs = [

    pytestCheckHook

  ];

  nativeCheckInputs = [ pytestCheckHook ];



  disabledTests = [

    # looks for missing data:

    # Test looks for missing data

    "test_config_filename"

    # regression associated with formulaic >= 0.6.0

    # Regression associated with formulaic >= 0.6.0

    # (see https://github.com/bids-standard/pybids/issues/1000)

    "test_split"

    # AssertionError, TypeError

    "test_run_variable_collection_bad_length_to_df_all_dense_var"

    "test_extension_initial_dot"

    "test_to_df"

  ];



  meta = with lib; {

    description = "Python tools for querying and manipulating BIDS datasets";

    mainProgram = "pybids";

    homepage = "https://github.com/bids-standard/pybids";

    changelog = "https://github.com/bids-standard/pybids/blob/${version}/CHANGELOG.rst";

    license = licenses.mit;

    maintainers = with maintainers; [ jonringer ];

    mainProgram = "pybids";

  };

}