Open
Description
Summary
As of Sphinx 1.3, the autodoc module allows setting a list of modules to be mocked. However, our extension does not read that list and some workflows will crash.
Actual behavior
From mriqc builds at readthedocs:
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
from ._conv import register_converters as _register_converters
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/anatomical.py:docstring of mriqc.workflows.anatomical:23: WARNING: Exception occurred in plotting workflows-1
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/anat/__init__.py", line 6, in <module>
from ..interfaces import mni # for backwards compatibility
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/interfaces/__init__.py", line 6, in <module>
from .masks import BETRPT as BET
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/interfaces/masks.py", line 25, in <module>
fsl.preprocess.BETInputSpec):
TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/anatomical.py:docstring of mriqc.workflows.anatomical.anat_qc_workflow:5: WARNING: Exception occurred in plotting workflows-2
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/anatomical.py", line 506, in airmsk_wf
interpolation='Linear', float=True), name='invert_xfm')
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 153, in __init__
raise IOError('interface must be an instance of an Interface')
OSError: interface must be an instance of an Interface
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/anatomical.py:docstring of mriqc.workflows.anatomical.gradient_threshold:1: WARNING: Exception occurred in plotting workflows-3
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 8, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/anatomical.py", line 95, in anat_qc_workflow
hmsk = headmsk_wf()
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/anatomical.py", line 448, in headmsk_wf
bet = pe.Node(fsl.BET(surfaces=True), name='fsl_bet')
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 153, in __init__
raise IOError('interface must be an instance of an Interface')
OSError: interface must be an instance of an Interface
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/anatomical.py:docstring of mriqc.workflows.anatomical.spatial_normalization:1: WARNING: Exception occurred in plotting workflows-4
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/anatomical.py", line 250, in compute_iqms
fwhm_interface = get_fwhmx()
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/utils.py", line 172, in get_fwhmx
afni_version = StrictVersion('%s.%s.%s' % Info.version())
TypeError: not enough arguments for format string
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:144: WARNING: Exception occurred in plotting workflows-5
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/anatomical.py", line 448, in headmsk_wf
bet = pe.Node(fsl.BET(surfaces=True), name='fsl_bet')
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 153, in __init__
raise IOError('interface must be an instance of an Interface')
OSError: interface must be an instance of an Interface
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py:docstring of mriqc.workflows.functional.compute_iqms:3: WARNING: Exception occurred in plotting workflows-7
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py", line 225, in compute_iqms
mem_gb=biggest_file_gb * 3)
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 153, in __init__
raise IOError('interface must be an instance of an Interface')
OSError: interface must be an instance of an Interface
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py:docstring of mriqc.workflows.functional.fmri_bmsk_workflow:5: WARNING: Exception occurred in plotting workflows-8
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py", line 688, in epi_mni_align
from niworkflows.interfaces.registration import (
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/interfaces/__init__.py", line 6, in <module>
from .masks import BETRPT as BET
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/interfaces/masks.py", line 25, in <module>
fsl.preprocess.BETInputSpec):
TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py:docstring of mriqc.workflows.functional.hmc_afni:1: WARNING: Exception occurred in plotting workflows-9
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py", line 470, in fmri_bmsk_workflow
outputtype='NIFTI_GZ'), name='afni_msk')
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 153, in __init__
raise IOError('interface must be an instance of an Interface')
OSError: interface must be an instance of an Interface
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py:docstring of mriqc.workflows.functional.individual_reports:1: WARNING: Exception occurred in plotting workflows-10
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 7, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py", line 89, in fmri_qc_workflow
name="non_steady_state_detector")
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 153, in __init__
raise IOError('interface must be an instance of an Interface')
OSError: interface must be an instance of an Interface
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:151: WARNING: Exception occurred in plotting workflows-11
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py", line 573, in hmc_afni
gen_ref = pe.Node(nwr.EstimateReferenceImage(mc_method="AFNI"), name="gen_ref")
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 153, in __init__
raise IOError('interface must be an instance of an Interface')
OSError: interface must be an instance of an Interface
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:178: WARNING: Exception occurred in plotting workflows-12
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py", line 512, in hmc_mcflirt
gen_ref = pe.Node(nwr.EstimateReferenceImage(mc_method="AFNI"), name="gen_ref")
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 153, in __init__
raise IOError('interface must be an instance of an Interface')
OSError: interface must be an instance of an Interface
/home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:204: WARNING: Exception occurred in plotting workflows-13
from /home/docs/checkouts/readthedocs.org/user_builds/mriqc/checkouts/master/docs/source/workflows.rst:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/sphinxext/plot_workflow.py", line 485, in run_code
exec(code, ns)
File "<string>", line 2, in <module>
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/mriqc/workflows/functional.py", line 349, in individual_reports
bigplot = pe.Node(FMRISummary(), name='BigPlot', mem_gb=biggest_file_gb * 3.5)
File "/home/docs/checkouts/readthedocs.org/user_builds/mriqc/envs/master/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 153, in __init__
raise IOError('interface must be an instance of an Interface')
OSError: interface must be an instance of an Interface
Expected behavior
No exceptions raised.
How to replicate the behavior
MRIQC
Script/Workflow details
Please put URL to code or code here (if not too long).
Platform details:
Read the docs