[BUG] CI failures for website build

[alessandrofelder]

CI seems to break for reasons unrelated to changes in two recent PR, and on current main

See #465

/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/downloads/brainglobe-atlasapi/brainglobe_atlasapi/atlas_generation/volume_utils.py:docstring of brainglobe_atlasapi.atlas_generation.volume_utils.create_masked_array:14: WARNING: Inline interpreted text or phrase reference start-string without end-string. [docutils]
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/downloads/brainglobe-atlasapi/brainglobe_atlasapi/utils.py:docstring of brainglobe_atlasapi.utils.check_internet_connection:3: ERROR: Unexpected indentation. [docutils]
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/downloads/brainglobe-atlasapi/brainglobe_atlasapi/utils.py:docstring of brainglobe_atlasapi.utils.check_internet_connection:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/source/index.md:51: WARNING: toctree contains reference to nonexisting document 'blackcap' [toc.not_readable]
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/source/tutorials/index.md:139: WARNING: toctree contains reference to nonexisting document 'api_examples/brainglobe_atlasapi' [toc.not_readable]
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/source/tutorials/index.md:: WARNING: image file not readable: api_examples/images/thumb/sphx_glr_brainglobe_atlasapi_thumb.png [image.not_readable]

And #493

/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/downloads/brainglobe-atlasapi/brainglobe_atlasapi/atlas_generation/volume_utils.py:docstring of brainglobe_atlasapi.atlas_generation.volume_utils.create_masked_array:14: WARNING: Inline interpreted text or phrase reference start-string without end-string. [docutils]
reading sources... [100%] tutorials/visualise-atlas-napari
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/downloads/brainglobe-atlasapi/brainglobe_atlasapi/utils.py:docstring of brainglobe_atlasapi.utils.check_internet_connection:3: ERROR: Unexpected indentation. [docutils]
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/downloads/brainglobe-atlasapi/brainglobe_atlasapi/utils.py:docstring of brainglobe_atlasapi.utils.check_internet_connection:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/source/index.md:51: WARNING: toctree contains reference to nonexisting document 'blackcap' [toc.not_readable]
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/source/tutorials/index.md:160: WARNING: toctree contains reference to nonexisting document 'api_examples/brainglobe_atlasapi' [toc.not_readable]
/home/runner/work/brainglobe.github.io/brainglobe.github.io/docs/source/tutorials/index.md:: WARNING: image file not readable: api_examples/images/thumb/sphx_glr_brainglobe_atlasapi_thumb.png [image.not_readable]

[alessandrofelder]

I cannot easily reproduce locally but will investigate further

[alessandrofelder]

Maybe it's as simple as

• some underlying library updated, presumably [doc-utils]
• this is therefore now more strict and we should update the docstrings on brainglobe-atlasapi to satisfy this.

But this doesn't explain why CI on #496 passes 🤔 (unless the explicit call to the setup function also matters?!)

[IgorTatarnikov]

Could the failures be related the linkcheck timeouts? Perhaps we should think about adding GIN to linkcheck ignore?

[IgorTatarnikov]

The error has been occurring but it doesn't usually block the run.

I've raised brainglobe/brainglobe-atlasapi#811 to fix the offending docstring!

[alessandrofelder]

Thanks for relating this to linkcheck timeouts on GIN - I did not manage to get there yesterday 😅

Perhaps we should think about adding GIN to linkcheck ignore?

I would say so. Especially if this happens on main this will mean changes we want are not propagated to the website