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aeye-lab / pymovements

A python package for processing eye movement data
https://pymovements.readthedocs.io
MIT License
57 stars 11 forks source link

readthe docs documentation build failing #694

Closed dkrako closed 3 months ago

dkrako commented 4 months ago

Current Behavior

Readthedocs fails during building the documentation.

Expected Behavior

No fail.

Minimum acceptance criteria

Failure Information (for bugs)

python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.2.6
initializing sphinxcontrib.datatemplates
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/bibliography.bib... parsed 12 entries
[autosummary] generating autosummary for: advanced-installation.rst, bibliography.rst, getting-started.rst, index.rst, reference/index.rst, tutorials/R-tutorial.md, tutorials/detecting-events.ipynb, tutorials/event-properties.ipynb, tutorials/heatmap.ipynb, tutorials/index.rst, tutorials/local-dataset.ipynb, tutorials/plot-main-sequence.ipynb, tutorials/preprocessing-raw-data.ipynb, tutorials/public-datasets.ipynb, tutorials/pymovements-in-10-minutes.ipynb, tutorials/saving-loading-events.ipynb, tutorials/saving-loading-preprocessed.ipynb
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.datasets.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.events.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.gaze.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.plotting.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.synthetic.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.DatasetDefinition.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.DatasetLibrary.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.DatasetPaths.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.datasets.GazeBase.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.datasets.GazeBaseVR.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.datasets.GazeGraph.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.datasets.GazeOnFaces.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.datasets.HBN.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.datasets.JuDo1000.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.plotting.traceplot.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.plotting.tsplot.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.synthetic.step_function.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.archives.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.checks.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.decorators.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.downloads.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.filters.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.parsing.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.paths.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.__init__.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.apply.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.clear_events.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.compute_event_properties.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.compute_properties.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.detect.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.detect_events.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.download.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.extract.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.dataset.Dataset.load.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.downloads.download_and_extract_archive.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.downloads.download_file.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.filters.events_split_nans.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.filters.filter_candidates_remove_nans.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.parsing.check_nan.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.parsing.compile_patterns.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.parsing.get_additional_columns.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.parsing.parse_eyelink.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.paths.get_filepaths.rst, /home/docs/checkouts/readthedocs.org/user_builds/pymovements/checkouts/latest/docs/source/reference/pymovements.utils.paths.match_filepaths.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 17 source files that are out of date
updating environment: [new config] 160 added, 0 changed, 0 removed
reading sources... [  1%] advanced-installation
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reading sources... [  2%] getting-started
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reading sources... [  9%] reference/pymovements.dataset.Dataset.download
reading sources... [ 10%] reference/pymovements.dataset.Dataset.extract
reading sources... [ 11%] reference/pymovements.dataset.Dataset.load
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reading sources... [ 23%] reference/pymovements.dataset.DatasetPaths.raw_to_event_filepath
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reading sources... [ 36%] reference/pymovements.datasets.ToyDatasetEyeLink
reading sources... [ 36%] reference/pymovements.datasets.ToyDatasetEyeLink.__init__
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reading sources... [ 42%] reference/pymovements.events.amplitude
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/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.5).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
  nbconvert.utils.pandoc.check_pandoc_version()
reading sources... [ 94%] tutorials/event-properties
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reading sources... [ 96%] tutorials/local-dataset
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reading sources... [ 98%] tutorials/preprocessing-raw-data
reading sources... [ 98%] tutorials/public-datasets
reading sources... [ 99%] tutorials/pymovements-in-10-minutes

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py", line 618, in parse
    rststring, resources = exporter.from_notebook_node(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py", line 397, in from_notebook_node
    nb, resources = pp.preprocess(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 101, in preprocess
    self.preprocess_cell(cell, resources, index)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 122, in preprocess_cell
    cell = self.execute_cell(cell, index, store_history=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
    return loop.run_until_complete(inner)
  File "/home/docs/.asdf/installs/python/3.9.18/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
    return future.result()
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/nbclient/client.py", line 1009, in async_execute_cell
    raise DeadKernelError("Kernel died") from None
nbclient.exceptions.DeadKernelError: Kernel died

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/sphinx/cmd/build.py", line 298, in build_main
    app.build(args.force_all, args.filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/sphinx/application.py", line 355, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 293, in build_update
    self.build(to_build,
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 313, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 420, in read
    self._read_serial(docnames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 441, in _read_serial
    self.read_doc(docname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 498, in read_doc
    publisher.publish()
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/docutils/core.py", line 234, in publish
    self.document = self.reader.read(self.source, self.parser,
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/sphinx/io.py", line 105, in read
    self.parse()
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/docutils/readers/__init__.py", line 76, in parse
    self.parser.parse(self.input, document)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py", line 627, in parse
    raise NotebookError(type(e).__name__ + ' in ' +
nbsphinx.NotebookError: DeadKernelError in tutorials/pymovements-in-10-minutes.ipynb:
Kernel died

Notebook error:
DeadKernelError in tutorials/pymovements-in-10-minutes.ipynb:
Kernel died
Command time: 421s Return: 2

The commit this started to appear is the following: feat: trialize gaze.detect() (#655)

As the kernel is also dying during calculating the event properties, I'm worried that my implementation caused a bug

dkrako commented 4 months ago

I think the problem is that we extend the reserved RAM usage at readthedocs, and #655 probably increased memory usage with the partition_by() call.

The strange thing is, that we only use the ToyDataset in the tutorial notebooks which doesn't have any groupby at all. But then, probably there are trial columns added during dataset intialization so we get a single partition when calling partition_by() in that case. #631 could help us to make a step forward to add a way to disable adding the parsed filename level information to a GazeDataFrame.

The other strange thing is that this really is not a lot of data in the ToyDataset example..

dkrako commented 4 months ago

Maybe the issue is more in this part:

/home/docs/checkouts/readthedocs.org/user_builds/pymovements/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.5).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
  nbconvert.utils.pandoc.check_pandoc_version()

readthedocs has pandoc 2.5 installed here, and nbconvert expects 2.14, so that could be an issue.

EDIT: Probably not, this line is also included in the log for builds that passed a month ago.

dkrako commented 4 months ago

It's always the 10 minute tutorial when the kernel dies, let's try to find the cell(s) that lead to the dead kernel.