Is pybids a mandatory dependency? #3223

liamtimms · 2020-06-04T15:50:32Z

Summary

Hi all,

I am packaging the newest nipype version and using the test function pytest -v --doctest-modules nipype. I have everything in requirements.txt installed and everything seems great in this new release. However, I am getting 1 failed test and it's in the BIDS functionality (which I have not chosen to include on my system at this time). Is pybids an optional dependency or a mandatory one? If mandatory I will install it, if optional should the test be skipped?

Thanks!

Actual behavior

the test output is:

========================================= FAILURES ==========================================
______________________ [doctest] nipype.interfaces.io.BIDSDataGrabber _______________________
2893 BIDS datagrabber module that wraps around pybids to allow arbitrary
2894     querying of BIDS datasets.
2895 
2896     Examples
2897     --------
2898     By default, the BIDSDataGrabber fetches anatomical and functional images
2899     from a project, and makes BIDS entities (e.g. subject) available for
2900     filtering outputs.
2901 
2902     >>> bg = BIDSDataGrabber()
UNEXPECTED EXCEPTION: ModuleNotFoundError("No module named 'bids'")
Traceback (most recent call last):
  File "/usr/lib/python3.8/doctest.py", line 1336, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest nipype.interfaces.io.BIDSDataGrabber[0]>", line 1, in <module>
  File "/mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/interfaces/io.py", line 2951, in __init__
    from bids import layout as bidslayout
ModuleNotFoundError: No module named 'bids'

Expected behavior

I would expect the BIDS related tests to be skipped if pybids, bids-validator, etc. are not installed.

Script/Workflow details

here is the full test summary if you are interested:

test results

========================================= FAILURES ==========================================
______________________ [doctest] nipype.interfaces.io.BIDSDataGrabber _______________________
2893 BIDS datagrabber module that wraps around pybids to allow arbitrary
2894     querying of BIDS datasets.
2895 
2896     Examples
2897     --------
2898     By default, the BIDSDataGrabber fetches anatomical and functional images
2899     from a project, and makes BIDS entities (e.g. subject) available for
2900     filtering outputs.
2901 
2902     >>> bg = BIDSDataGrabber()
UNEXPECTED EXCEPTION: ModuleNotFoundError("No module named 'bids'")
Traceback (most recent call last):
  File "/usr/lib/python3.8/doctest.py", line 1336, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest nipype.interfaces.io.BIDSDataGrabber[0]>", line 1, in <module>
  File "/mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/interfaces/io.py", line 2951, in __init__
    from bids import layout as bidslayout
ModuleNotFoundError: No module named 'bids'
/mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/interfaces/io.py:2902: UnexpectedException
----------------------------------- Captured stdout call ------------------------------------
200604-11:31:33,297 nipype.interface WARNING:
	 Unable to import ['bids']; BIDSDataGrabber interface may fail to run
------------------------------------- Captured log call -------------------------------------
WARNING  nipype.interface:core.py:1069 Unable to import ['bids']; BIDSDataGrabber interface may fail to run
===================================== warnings summary ======================================
/usr/lib/python3.8/site-packages/dipy/viz/__init__.py:21
  /usr/lib/python3.8/site-packages/dipy/viz/__init__.py:21: UserWarning: You do not have FURY installed. Some visualization functions might not work for you. For installation instructions, please visit: https://fury.gl/
    warnings.warn(

/usr/lib/python3.8/site-packages/dipy/stats/__init__.py:7
  /usr/lib/python3.8/site-packages/dipy/stats/__init__.py:7: UserWarning: The `dipy.stats` module is still under heavy development and functionality, as well as the API is likely to change in future versions of the software
    warnings.warn(w_string)

nipype/interfaces/mrtrix/convert.py:6
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/interfaces/mrtrix/convert.py:6: DeprecationWarning: The trackvis interface has been deprecated and will be removed in v4.0; please use the 'nibabel.streamlines' interface.
    import nibabel.trackvis as trk

nipype/pipeline/engine/tests/test_nodes.py:319
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/pipeline/engine/tests/test_nodes.py:319: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html
    @pytest.mark.timeout(30)

nipype/pipeline/plugins/tests/test_oar.py:33
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/pipeline/plugins/tests/test_oar.py:33: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html
    @pytest.mark.timeout(60)

nipype/pipeline/plugins/tests/test_pbs.py:33
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/pipeline/plugins/tests/test_pbs.py:33: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html
    @pytest.mark.timeout(60)

/usr/lib/python3.8/site-packages/sphinxcontrib/napoleon/docstring.py:16
  /usr/lib/python3.8/site-packages/sphinxcontrib/napoleon/docstring.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will stop working
    from collections import Callable

nipype/utils/tests/test_provenance.py:18
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/utils/tests/test_provenance.py:18: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html
    @pytest.mark.timeout(60)

nipype/utils/tests/test_provenance.py:31
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/utils/tests/test_provenance.py:31: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html
    @pytest.mark.timeout(60)

nipype/workflows/__init__.py:28
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/workflows/__init__.py:28: UserWarning: Nipype 1 workflows have been moved to the niflow-nipype1-workflows package. pip install niflow-nipype1-workflows to continue using them.
    warnings.warn(" ".join(_msg))

algorithms/tests/test_CompCor.py::TestCompCor::test_tcompcor_asymmetric_dim
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/algorithms/confounds.py:1438: RuntimeWarning: invalid value encountered in true_divide
    variance_explained = (s ** 2) / np.sum(s ** 2)

interfaces/fsl/dti.py::nipype.interfaces.fsl.dti.ProbTrackX
interfaces/fsl/dti.py::nipype.interfaces.fsl.dti.ProbTrackX2
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/interfaces/fsl/dti.py:816: DeprecationWarning: Deprecated: Please use create_bedpostx_pipeline instead
    warnings.warn(

interfaces/fsl/epi.py::nipype.interfaces.fsl.epi.EPIDeWarp
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/interfaces/fsl/epi.py:1417: DeprecationWarning: Deprecated: Please use niflow.nipype1.workflows.dmri.preprocess.epi.sdc_fmb instead
    warnings.warn(

interfaces/fsl/epi.py::nipype.interfaces.fsl.epi.EddyCorrect
interfaces/fsl/tests/test_epi.py::test_eddy_correct2
interfaces/fsl/tests/test_epi.py::test_eddy_correct2
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/interfaces/fsl/epi.py:1523: DeprecationWarning: Deprecated: Please use nipype.interfaces.fsl.epi.Eddy instead
    warnings.warn(

interfaces/nipy/utils.py::nipype.interfaces.nipy.utils.Similarity
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/interfaces/nipy/utils.py:59: DeprecationWarning: This interface is deprecated since 0.10.0. Please use nipype.algorithms.metrics.Similarity
    warnings.warn(

interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extract_no_shared
  /usr/lib/python3.8/site-packages/nilearn/_utils/niimg.py:168: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will stop working
    if isinstance(niimgs, collections.Iterable):

interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extract_no_shared
interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_global_no_shared
interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_global_no_shared
interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_4d_global_no_shared
interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_traits_valid
  /usr/lib/python3.8/site-packages/nilearn/_utils/cache_mixin.py:226: DeprecationWarning: The 'cachedir' attribute has been deprecated in version 0.12 and will be removed in version 0.14.
  Use os.path.join(memory.location, 'joblib') attribute instead.
    if (memory.cachedir is None and memory_level is not None

interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_equiv_4d_no_shared
interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_4d_no_shared
interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_4d_global_no_shared
interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_shared
interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_shared
interfaces/tests/test_nilearn.py::TestSignalExtraction::test_signal_extr_shared
  /usr/lib/python3.8/site-packages/nilearn/_utils/cache_mixin.py:295: DeprecationWarning: The 'cachedir' attribute has been deprecated in version 0.12 and will be removed in version 0.14.
  Use os.path.join(memory.location, 'joblib') attribute instead.
    if self.memory_level == 0 and self.memory.cachedir is not None:

utils/tests/test_misc.py::test_rgetcwd
  /mnt/4e43a4f6-7402-4881-bcf5-d280e54cc385/AUR/aur/python-nipype/src/nipype-1.5.0/nipype/utils/misc.py:368: UserWarning: Current folder does not exist, replacing with "/tmp/pytest-of-mri/pytest-1/test_rgetcwd0" instead.
    warn('Current folder does not exist, replacing with "%s" instead.' % cwd)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
================================== short test summary info ==================================
FAILED nipype/interfaces/io.py::nipype.interfaces.io.BIDSDataGrabber
====== 1 failed, 2809 passed, 73 skipped, 5 xfailed, 31 warnings in 153.19s (0:02:33) =======

Platform details:

(have not yet installed 1.5.0)

200604-11:38:58,673 nipype.utils INFO:
	 Running nipype version 1.4.2 (latest: 1.5.0)
{'commit_hash': '%h',
 'commit_source': 'archive substitution',
 'networkx_version': '2.4',
 'nibabel_version': '3.1.0',
 'nipype_version': '1.4.2',
 'numpy_version': '1.18.3',
 'pkg_path': '/usr/lib/python3.8/site-packages/nipype',
 'scipy_version': '1.4.1',
 'sys_executable': '/usr/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.8.3 (default, May 17 2020, 18:15:42) \n[GCC 10.1.0]',
 'traits_version': '6.0.0'}

Execution environment

Choose one

My python environment outside container

The text was updated successfully, but these errors were encountered:

effigies · 2020-06-04T15:56:27Z

No. We should condition those tests on whether it's available.

effigies · 2020-06-04T16:01:43Z

Oh, it's the doctest. The regular tests are conditioned.

effigies · 2020-06-04T20:45:59Z

@liamtimms Do you need a bug-fix release in order to package? Or can you include #3224 as a patch?

liamtimms · 2020-06-04T20:57:15Z

Hi @effigies thank you for the quick fix and response! Patching should definitely be sufficient for this release. I'll test that now.

liamtimms · 2020-06-04T22:03:24Z

=============== 2809 passed, 74 skipped, 5 xfailed, 35 warnings in 157.02s (0:02:37) ===========

cheers, thanks!

effigies mentioned this issue Jun 4, 2020

DOC: Skip BIDSDataGrabber doctest if pybids is missing #3224

Merged

1 task

liamtimms added a commit to liamtimms/aur that referenced this issue Jun 4, 2020

adding patch from nipy/nipype#3223

7353979

liamtimms closed this as completed Jun 4, 2020

archlinux-github pushed a commit to archlinux/aur that referenced this issue Jul 30, 2022

adding patch (see: nipy/nipype#3223) and check function

d8929d5

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Is pybids a mandatory dependency? #3223

Is pybids a mandatory dependency? #3223

liamtimms commented Jun 4, 2020 •

edited

Loading

effigies commented Jun 4, 2020

effigies commented Jun 4, 2020

effigies commented Jun 4, 2020

liamtimms commented Jun 4, 2020

liamtimms commented Jun 4, 2020

Is pybids a mandatory dependency? #3223

Is pybids a mandatory dependency? #3223

Comments

liamtimms commented Jun 4, 2020 • edited Loading

Summary

Actual behavior

Expected behavior

Script/Workflow details

Platform details:

Execution environment

effigies commented Jun 4, 2020

effigies commented Jun 4, 2020

effigies commented Jun 4, 2020

liamtimms commented Jun 4, 2020

liamtimms commented Jun 4, 2020

liamtimms commented Jun 4, 2020 •

edited

Loading