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NeurodataWithoutBorders / pynwb

A Python API for working with Neurodata stored in the NWB Format
https://pynwb.readthedocs.io
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[Documentation]: cannot build documentation locally #1441

Closed bendichter closed 2 years ago

bendichter commented 2 years ago

What would you like changed or added to the documentation and why?

sphinx-build -a docs/source build
Running Sphinx v4.4.0
loading pickled environment... done
generating gallery...
Using Sphinx-Gallery to convert rst text blocks to markdown for .ipynb files.
generating gallery for tutorials/general... [100%] parallel_io.py                                                                          
generating gallery for tutorials/domain... [100%] plot_icephys_pandas.py                                                                   
generating gallery for tutorials/advanced_io... [100%] streaming.py                                                                        
computation time summary:
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.base.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.behavior.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.core.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.device.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.ecephys.rst.
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Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.image.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.misc.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.ogen.rst.
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Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.scratch.rst.
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Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.base.rst.
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Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.core.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.ecephys.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.epoch.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.file.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.icephys.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.image.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.misc.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.ogen.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.io.ophys.rst.
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Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.map.rst.
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Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.base.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.behavior.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.ecephys.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.epoch.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.file.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.icephys.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.image.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.misc.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.ogen.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.ophys.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.legacy.io.retinotopy.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.testing.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.testing.icephys_testutils.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.testing.make_test_files.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.testing.testh5io.rst.
Creating file /Users/bendichter/dev/pynwb/docs/source/pynwb.testing.utils.rst.
building [mo]: all of 0 po files
building [html]: all source files
updating environment: 0 added, 2 changed, 0 removed
reading sources... [100%] tutorials/index                                                                                                  
WARNING: autodoc: failed to import module 'scratch' from module 'pynwb'; the following exception was raised:
No module named 'dandi'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /Users/bendichter/dev/pynwb/docs/source/modules.rst: WARNING: document isn't included in any toctree
/Users/bendichter/dev/pynwb/docs/source/overview_nwbfile.rst: WARNING: document isn't included in any toctree
/Users/bendichter/dev/pynwb/docs/source/tutorials/general/advanced_hdf5_io.rst: WARNING: document isn't included in any toctree
/Users/bendichter/dev/pynwb/docs/source/tutorials/general/iterative_write.rst: WARNING: document isn't included in any toctree
/Users/bendichter/dev/pynwb/docs/source/tutorials/general/linking_data.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] validation                                                                                                        
docs/CONTRIBUTING.rst:9: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/.github/CODE_OF_CONDUCT.rst' could be replaced by an extlink (try using ':pynwb:`blob/dev/.github/CODE_OF_CONDUCT.rst`' instead)
docs/CONTRIBUTING.rst:25: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/issues' could be replaced by an extlink (try using ':pynwb:`issues`' instead)
docs/CONTRIBUTING.rst:100: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/labels' could be replaced by an extlink (try using ':pynwb:`labels`' instead)
docs/CONTRIBUTING.rst:108: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/milestones' could be replaced by an extlink (try using ':pynwb:`milestones`' instead)
/Users/bendichter/dev/pynwb/docs/source/software_process.rst:48: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/requirements-min.txt' could be replaced by an extlink (try using ':pynwb:`blob/dev/requirements-min.txt`' instead)
/Users/bendichter/dev/pynwb/docs/source/software_process.rst:51: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/requirements.txt' could be replaced by an extlink (try using ':pynwb:`blob/dev/requirements.txt`' instead)
/Users/bendichter/dev/pynwb/docs/source/software_process.rst:54: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/requirements-dev.txt' could be replaced by an extlink (try using ':pynwb:`blob/dev/requirements-dev.txt`' instead)
/Users/bendichter/dev/pynwb/docs/source/software_process.rst:58: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/requirements-doc.txt' could be replaced by an extlink (try using ':pynwb:`blob/dev/requirements-doc.txt`' instead)
/Users/bendichter/dev/pynwb/docs/source/software_process.rst:61: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/setup.py' could be replaced by an extlink (try using ':pynwb:`blob/dev/setup.py`' instead)
/Users/bendichter/dev/pynwb/docs/source/software_process.rst:82: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/releases' could be replaced by an extlink (try using ':pynwb:`releases`' instead)
/Users/bendichter/dev/pynwb/docs/source/tutorials/domain/ecephys.rst:388: WARNING: undefined label: basic_data_interfaces
/Users/bendichter/dev/pynwb/docs/source/tutorials/general/file.rst:26: WARNING: undefined label: basics_background
/Users/bendichter/dev/pynwb/docs/source/update_requirements.rst:10: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/requirements.txt' could be replaced by an extlink (try using ':pynwb:`blob/dev/requirements.txt`' instead)
/Users/bendichter/dev/pynwb/docs/source/update_requirements.rst:11: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/requirements-dev.txt' could be replaced by an extlink (try using ':pynwb:`blob/dev/requirements-dev.txt`' instead)
/Users/bendichter/dev/pynwb/docs/source/update_requirements.rst:12: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/requirements-doc.txt' could be replaced by an extlink (try using ':pynwb:`blob/dev/requirements-doc.txt`' instead)
/Users/bendichter/dev/pynwb/docs/source/update_requirements.rst:13: WARNING: hardcoded link 'https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/requirements-min.txt' could be replaced by an extlink (try using ':pynwb:`blob/dev/requirements-min.txt`' instead)
generating indices... genindex py-modindex done
highlighting module code... [100%] pynwb.validate                                                                                          
writing additional pages... search done
copying images... [100%] tutorials/advanced_io/images/thumb/sphx_glr_streaming_thumb.png                                                   
copying downloadable files... [100%] ../tutorials/tutorials_jupyter.zip                                                                    
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 22 warnings.

The HTML pages are in build.

Sphinx-Gallery successfully executed 0 out of 0 files subselected by:

    gallery_conf["filename_pattern"] = '/plot'
    gallery_conf["ignore_pattern"]   = '__init__\\.py'

after excluding 2 files that had previously been run (based on MD5).

embedding documentation hyperlinks...
embedding documentation hyperlinks for tutorials... [  9%] iterative_write.html                                                            
Extension error (sphinx_gallery.docs_resolv):
Handler <function embed_code_links at 0x7ff488974c10> for event 'build-finished' threw an exception (exception: string indices must be integers)
(pynwb-docs) MacBook-Pro-3:pynwb bendichter$ pip freeze
aiohttp==3.7.4
alabaster==0.7.12
allensdk==2.13.4
argschema==3.0.1
async-timeout==3.0.1
attrs==21.4.0
Babel==2.9.1
boto3==1.17.21
botocore==1.20.112
cachetools==4.2.4
certifi==2021.10.8
chardet==3.0.4
charset-normalizer==2.0.12
cloudpickle @ file:///tmp/build/80754af9/cloudpickle_1632508026186/work
cycler @ file:///tmp/build/80754af9/cycler_1637851556182/work
cytoolz==0.11.0
dask @ file:///opt/conda/conda-bld/dask-core_1647268715755/work
distro==1.7.0
docutils==0.17.1
fonttools==4.25.0
fsspec @ file:///opt/conda/conda-bld/fsspec_1647268051896/work
future==0.18.2
Glymur==0.8.19
greenlet==1.1.2
h5py==3.6.0
hdmf==3.2.1
idna==3.3
imagecodecs @ file:///opt/concourse/worker/volumes/live/e941b486-3a75-48c0-6296-0718ca963055/volume/imagecodecs_1635529114027/work
imageio @ file:///tmp/build/80754af9/imageio_1617700267927/work
imagesize==1.3.0
importlib-metadata==4.11.3
importlib-resources==5.4.0
Jinja2==2.11.3
jmespath==0.10.0
jsonschema==4.4.0
kiwisolver @ file:///Users/builder/miniconda3/envs/prefect/conda-bld/kiwisolver_1638569885739/work
locket @ file:///opt/concourse/worker/volumes/live/f41c22bc-62f0-495b-47b6-9ceffe265d54/volume/locket_1647006006948/work
MarkupSafe==2.0.1
marshmallow==3.15.0
matplotlib==3.4.2
mkl-fft==1.3.1
mkl-random @ file:///opt/concourse/worker/volumes/live/f196a661-8e33-4aac-63bc-efb2ff50e035/volume/mkl_random_1626186080069/work
mkl-service==2.4.0
multidict==6.0.2
munkres==1.1.4
ndx-events==0.2.0
nest-asyncio==1.5.4
networkx @ file:///opt/conda/conda-bld/networkx_1647437648384/work
numexpr==2.8.1
numpy @ file:///opt/concourse/worker/volumes/live/ceac9fd4-1ae1-48f8-612a-0c99bf783d0e/volume/numpy_and_numpy_base_1634106709647/work
packaging @ file:///tmp/build/80754af9/packaging_1637314298585/work
pandas==1.4.1
partd @ file:///opt/conda/conda-bld/partd_1647245470509/work
patsy==0.5.2
Pillow==9.0.1
psycopg2-binary==2.9.3
Pygments==2.11.2
pynrrd==0.4.2
pynwb==2.0.1
pyparsing @ file:///tmp/build/80754af9/pyparsing_1635766073266/work
pyrsistent==0.18.1
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
pytz==2021.3
PyWavelets @ file:///opt/concourse/worker/volumes/live/ea36e10f-66e8-43ae-511e-c4092764493f/volume/pywavelets_1601658378672/work
PyYAML==6.0
requests==2.27.1
requests-toolbelt==0.9.1
ruamel.yaml==0.17.21
ruamel.yaml.clib==0.2.6
s3transfer==0.3.7
scikit-build==0.13.1
scikit-image==0.16.2
scipy @ file:///opt/concourse/worker/volumes/live/7554f9b4-1616-4d3d-50f8-914545975614/volume/scipy_1641555024289/work
seaborn==0.11.2
semver==2.13.0
SimpleITK==2.1.1
simplejson==3.17.6
six @ file:///tmp/build/80754af9/six_1644875935023/work
snowballstemmer==2.2.0
Sphinx==4.4.0
sphinx-gallery==0.10.1
sphinx-rtd-theme==1.0.0
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
SQLAlchemy==1.4.32
statsmodels==0.13.0
tables==3.6.1
tifffile @ file:///tmp/build/80754af9/tifffile_1627275862826/work
toolz @ file:///tmp/build/80754af9/toolz_1636545406491/work
tqdm==4.63.0
typing_extensions==4.1.1
urllib3==1.26.9
xarray==0.15.1
yarl==1.7.2
zipp==3.7.0

Do you have any interest in helping write or edit the documentation?

Yes, but I would need guidance.

Code of Conduct

bendichter commented 2 years ago

@rly , could you help with this? Is it a sphinx version issue?

bendichter commented 2 years ago

running sphinx-build -a source build from within the docs directory worked