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Doc builds broken #414

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effigies opened this issue Dec 14, 2023 · 2 comments · Fixed by #427 or #428
Closed

Doc builds broken #414

effigies opened this issue Dec 14, 2023 · 2 comments · Fixed by #427 or #428
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bug Something isn't working

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@effigies
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What happened?

#408 broke the doc builds.

What command did you use?

make -C docs/ SPHINXOPTS="-W" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html

What version of the software are you running?

master

How are you running this software?

Other

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

make: Entering directory '/home/runner/work/sdcflows/sdcflows/docs'
PYTHONPATH=/home/runner/work/sdcflows/sdcflows SPHINX_APIDOC_OPTIONS=members,show-inheritance sphinx-build -b html -d /home/runner/docs/doctrees  -W . /home/runner/docs/master
Running Sphinx v7.2.6
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv...
loading intersphinx inventory from https://matplotlib.org/stable/objects.inv...
loading intersphinx inventory from https://bids-standard.github.io/pybids/objects.inv...
loading intersphinx inventory from https://nipy.org/nibabel/objects.inv...
loading intersphinx inventory from https://nipype.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://www.nipreps.org/niworkflows/objects.inv...
loading intersphinx inventory from https://www.nipreps.org/smriprep/objects.inv...
loading intersphinx inventory from https://www.templateflow.org/python-client/objects.inv...
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.config.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.fieldmaps.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.transform.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.cli.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.cli.main.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.cli.parser.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.cli.workflow.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.data.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.interfaces.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.interfaces.brainmask.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.interfaces.bspline.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.interfaces.epi.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.interfaces.fmap.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.interfaces.reportlets.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.interfaces.utils.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.utils.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.utils.bimap.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.utils.epimanip.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.utils.misc.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.utils.phasemanip.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.utils.telemetry.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.utils.tools.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.utils.wrangler.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.viz.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.viz.utils.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.ancillary.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.base.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.outputs.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.apply.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.apply.correction.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.apply.registration.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.fit.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.fit.base.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.fit.fieldmap.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.fit.pepolar.rst.
Creating file /home/runner/work/sdcflows/sdcflows/docs/api/sdcflows.workflows.fit.syn.rst.
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 9 source files that are out of date
updating environment: [new config] 46 added, 0 changed, 0 removed
reading sources... [  2%] api
reading sources... [  4%] api/sdcflows.cli
reading sources... [  7%] api/sdcflows.cli.main
reading sources... [  9%] api/sdcflows.cli.parser
reading sources... [ 11%] api/sdcflows.cli.workflow
reading sources... [ 13%] api/sdcflows.config
reading sources... [ 15%] api/sdcflows.data
reading sources... [ 17%] api/sdcflows.fieldmaps
reading sources... [ 20%] api/sdcflows.interfaces
reading sources... [ 22%] api/sdcflows.interfaces.brainmask
reading sources... [ 24%] api/sdcflows.interfaces.bspline
reading sources... [ 26%] api/sdcflows.interfaces.epi
reading sources... [ 28%] api/sdcflows.interfaces.fmap
reading sources... [ 30%] api/sdcflows.interfaces.reportlets
reading sources... [ 33%] api/sdcflows.interfaces.utils
reading sources... [ 35%] api/sdcflows.transform
reading sources... [ 37%] api/sdcflows.utils
reading sources... [ 39%] api/sdcflows.utils.bimap
reading sources... [ 41%] api/sdcflows.utils.epimanip
reading sources... [ 43%] api/sdcflows.utils.misc
reading sources... [ 46%] api/sdcflows.utils.phasemanip
reading sources... [ 48%] api/sdcflows.utils.telemetry
reading sources... [ 50%] api/sdcflows.utils.tools
reading sources... [ 52%] api/sdcflows.utils.wrangler
reading sources... [ 54%] api/sdcflows.viz
reading sources... [ 57%] api/sdcflows.viz.utils
reading sources... [ 59%] api/sdcflows.workflows
reading sources... [ 61%] api/sdcflows.workflows.ancillary
reading sources... [ 63%] api/sdcflows.workflows.apply
reading sources... [ 65%] api/sdcflows.workflows.apply.correction
231214-14:25:09,919 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/unwarp_wf/sdcflows-workflows-apply-correction-1.png (graph2use=orig, simple_form=True).
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz

  0%|          | 0.00/29.6k [00:00<?, ?B/s]
100%|██████████| 29.6k/29.6k [00:00<00:00, 10.9MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg.nii.gz

  0%|          | 0.00/3.93M [00:00<?, ?B/s]
 56%|█████▌    | 2.19M/3.93M [00:00<00:00, 11.6MB/s]
100%|██████████| 3.93M/3.93M [00:00<00:00, 18.6MB/s]
231214-14:25:16,659 nipype.interface WARNING:
	 FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
231214-14:25:16,661 nipype.interface WARNING:
	 FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
231214-14:25:17,209 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/pepolar_estimate_wf/sdcflows-workflows-fit-pepolar-1.png (graph2use=orig, simple_form=True).
231214-14:25:17,445 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/pepolar_estimate_wf/sdcflows-workflows-fit-pepolar-1.svg (graph2use=orig, simple_form=True).
231214-14:25:17,712 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/pepolar_estimate_wf/sdcflows-workflows-fit-pepolar-1.pdf (graph2use=orig, simple_form=True).
231214-14:25:17,739 nipype.interface WARNING:
	 FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
231214-14:25:17,742 nipype.interface WARNING:
	 FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
231214-14:25:18,371 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/pepolar_estimate_wf/sdcflows-workflows-fit-pepolar-2.png (graph2use=orig, simple_form=True).
231214-14:25:18,621 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/pepolar_estimate_wf/sdcflows-workflows-fit-pepolar-2.svg (graph2use=orig, simple_form=True).
231214-14:25:18,890 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/pepolar_estimate_wf/sdcflows-workflows-fit-pepolar-2.pdf (graph2use=orig, simple_form=True).
reading sources... [ 80%] api/sdcflows.workflows.fit.syn
231214-14:25:19,639 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/syn_sdc_wf/sdcflows-workflows-fit-syn-1.png (graph2use=orig, simple_form=True).
231214-14:25:19,893 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/syn_sdc_wf/sdcflows-workflows-fit-syn-1.svg (graph2use=orig, simple_form=True).
231214-14:25:20,161 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/syn_sdc_wf/sdcflows-workflows-fit-syn-1.pdf (graph2use=orig, simple_form=True).
231214-14:25:20,848 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/syn_sdc_wf/sdcflows-workflows-fit-syn-2.png (graph2use=orig, simple_form=True).
231214-14:25:21,109 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/syn_sdc_wf/sdcflows-workflows-fit-syn-2.svg (graph2use=orig, simple_form=True).
231214-14:25:21,388 nipype.workflow INFO:
	 Generated workflow graph: /home/runner/docs/wf_directive/api/syn_sdc_wf/sdcflows-workflows-fit-syn-2.pdf (graph2use=orig, simple_form=True).
reading sources... [ 83%] api/sdcflows.workflows.outputs
reading sources... [ 85%] changes
reading sources... [ 87%] cli
reading sources... [ 89%] examples
reading sources... [ 91%] index
reading sources... [ 93%] installation
reading sources... [ 96%] links
reading sources... [ 98%] methods
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
reading sources... [100%] notebooks/SDC - Theory and physics

Warning, treated as error:
autodoc: failed to import module 'parser' from module 'sdcflows.cli'; the following exception was raised:
sdcflows
make: *** [Makefile:61: html] Error 2
make: Leaving directory '/home/runner/work/sdcflows/sdcflows/docs'
Error: Process completed with exit code 2.

Additional information / screenshots

Example CI failure: https://github.com/nipreps/sdcflows/actions/runs/7210198586/job/19642804807
@effigies effigies added the bug Something isn't working label Dec 14, 2023
@effigies effigies mentioned this issue Jan 18, 2024
Merged
oesteban added a commit that referenced this issue Jan 18, 2024
@oesteban
fix: pandoc requires texlive to render latex in notebook
4c939a7 
The new notebook has some latex insets, and I believe pandoc is
generating empty environments for them, which translate into warnings
assumed as errors.

It is the only difference I could think of between the environment in
CircleCI and the testing environment I've created on my workstation.

Resolves: #414.
@oesteban oesteban mentioned this issue Jan 18, 2024
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@oesteban
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Figured out the two problems:

  • texlive was missing (although I don't know this would only just make rendering ugly)
  • the notebook downloads one template from templateflow and nbsphinx was generating invalid RST (which is atm the intermediate conversion format).

I think the latter was the real problem here.

@effigies
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Thanks, Oscar.

@effigies effigies mentioned this issue Jan 18, 2024
Merged
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@effigies @oesteban