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@zmoon zmoon commented Sep 11, 2025

Building on #1354, resolving (hopefully) the current rest of the warnings in the docs build.

Addressing non-consecutive heading increase warnings, I had to edit notebook markdown, but there should be no change in the rendered output (except for 085d3de which I changed to match the other numbered headings).

Another aspect I wanted to note is the warnings about the application/vnd.holoviews_load.v0+json MIME type. I tried to find out (and experimented) to see if HoloViews could be convinced not to output this MIME type in notebook execution, but so far I was unsuccessful and elected to suppress the warning (only issue is that this suppresses all unknown MIME type warnings, not just for HoloViews). But maybe someone knows. Or a Myst-NB renderer plugin could be a solution.

to address these warnings:

uxarray/docs/getting-started/quick-overview.ipynb:20002: WARNING: Pygments lexer name 'ipython2' is not known

also removed `|` from end of heading
maybe from Furo?

WARNING: unsupported theme option 'navbar_footer_text' given
otherwise we get a lot of these from the HoloViews plots

For example:

uxarray/docs/getting-started/quick-overview.ipynb:150002: WARNING: skipping unknown output mime type: application/vnd.holoviews_load.v0+json [mystnb.unknown_mime_type] [mystnb.unknown_mime_type]
docs/contributing.rst: WARNING: document isn't included in any toctree
docs/examples/template.ipynb: WARNING: document isn't included in any toctree
docs/user-guide/custom-grid.ipynb: WARNING: document isn't included in any toctree
docs/user-guide/spatial-hashing.ipynb: WARNING: document isn't included in any toctree
docs/user-guide/template.ipynb: WARNING: document isn't included in any toctree
for example:

docs/api.rst:180: WARNING: Title underline too short.
uxarray/docs/contributing.rst:518: WARNING: Bullet list ends without a blank line; unexpected unindent. [docutils]
docs/contributing.rst:544: WARNING: Bullet list ends without a blank line; unexpect
uxarray/docs/contributing.rst:70: WARNING: Failed to create a cross reference. A title or caption not found: 'examples' [ref.ref]
uxarray/docs/contributing.rst:604: WARNING: undefined label: 'index' [ref.ref]
mainly bullet list issue
uxarray/docs/user-guide/gradients.ipynb.rst:10002: WARNING: Document headings start at H2, not H1 [myst.header]
as it was, they were just not showing up

docs/user-guide/data-structures.ipynb.rst:280008: WARNING: Unknown directive type: 'info' [myst.directive_unknown]
docs/user-guide/data-structures.ipynb.rst:370008: WARNING: Unknown directive type: 'info' [myst.directive_unknown]
https://myst-parser.readthedocs.io/en/stable/syntax/admonitions.html#admonition-types
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@philipc2 philipc2 linked an issue Sep 12, 2025 that may be closed by this pull request
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Nice work! Builds are looking warning-free.

https://app.readthedocs.org/projects/uxarray/builds/29549535/

@philipc2 philipc2 added the documentation Improvements or additions to documentation label Sep 12, 2025
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Another aspect I wanted to note is the warnings about the application/vnd.holoviews_load.v0+json MIME type. I tried to find out (and experimented) to see if HoloViews could be convinced not to output this MIME type in notebook execution, but so far I was unsuccessful and elected to suppress the warning (only issue is that this suppresses all unknown MIME type warnings, not just for HoloViews). But maybe someone knows. Or a Myst-NB renderer plugin could be a solution.

Appreciate you looking into this. @kafitzgerald have you encountered something like this before?

@philipc2 philipc2 merged commit 34f76bd into UXARRAY:main Sep 12, 2025
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Unfortunately, I haven't. I suspect because we're not using Holoviews.

I can try to look into this at some point though.

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It looks like something similar prompted this to be the warning suppression example in the MyST-NB docs: https://myst-nb.readthedocs.io/en/latest/configuration.html#warning-suppression

Given that, maybe we just leave as is.

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