DOC: remaining warnings from documentation build

[neutrinoceros]

Bug report

Bug summary

I started fixing the docs build in #3368, however, 37 warnings remain, which I will sort by categories here.
The reason fixing them is important is that it will make it possible to mark a build with a single warning as FAILED instead of PASSED, catching new mistakes much earlier.

Import errors

Looks to me that all of these would be solved by installing pyembree in the docs build. However, it seems to be only distributed via conda, and I don't think that conda is used here, so I don't know what to do.

WARNING: autodoc: failed to import module 'mesh_construction' from module 'yt.utilities.lib.embree_mesh'; the following exception was raised:
No module named 'yt.utilities.lib.embree_mesh.mesh_construction'
WARNING: autodoc: failed to import module 'mesh_intersection' from module 'yt.utilities.lib.embree_mesh'; the following exception was raised:
No module named 'yt.utilities.lib.embree_mesh.mesh_intersection'
WARNING: autodoc: failed to import module 'mesh_samplers' from module 'yt.utilities.lib.embree_mesh'; the following exception was raised:
No module named 'yt.utilities.lib.embree_mesh.mesh_samplers'
WARNING: autodoc: failed to import module 'mesh_traversal' from module 'yt.utilities.lib.embree_mesh'; the following exception was raised:
No module named 'yt.utilities.lib.embree_mesh.mesh_traversal'

"duplicate object description"

I currently have no idea how to solve these because I don't understand what the error message is pointing at.
On the plus side, all these warnings come in pairs, so there's half as much work as it seems.

docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.data_version:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.data_version, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.domain_width:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.domain_width, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.idx:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.idx, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.leafsize:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.leafsize, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.leaves:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.leaves, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.left_edge:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.left_edge, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.ndim:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.ndim, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.npts:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.npts, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.num_leaves:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.num_leaves, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.periodic:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.periodic, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyKDTree.right_edge:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyKDTree.right_edge, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.domain_width:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.domain_width, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.left_edge:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.left_edge, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.left_neighbors:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.left_neighbors, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.ndim:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.ndim, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.npts:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.npts, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.num_leaves:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.num_leaves, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.periodic_left:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.periodic_left, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.periodic_right:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.periodic_right, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.right_edge:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.right_edge, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.right_neighbors:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.right_neighbors, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.start_idx:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.start_idx, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them
docstring of yt.utilities.lib.cykdtree.kdtree.PyNode.stop_idx:1: WARNING: duplicate object description of yt.utilities.lib.cykdtree.kdtree.PyNode.stop_idx, other instance in reference/api/yt.utilities.lib.cykdtree.kdtree, use :noindex: for one of them

docstring mistakes

I've tried to fix these already, but failed. There's something I'm missing about rst + docstrings.

/var/jenkins_home/workspace/yt_docs_new/yt/utilities/lib/cykdtree/plot.py:docstring of yt.utilities.lib.cykdtree.plot.plot2D_serial:9: WARNING: Field list ends without a blank line; unexpected unindent.
/var/jenkins_home/workspace/yt_docs_new/yt/visualization/plot_modifications.py:docstring of yt.visualization.plot_modifications.ScaleCallback:59: WARNING: Unexpected indentation.
/var/jenkins_home/workspace/yt_docs_new/yt/visualization/plot_modifications.py:docstring of yt.visualization.plot_modifications.ScaleCallback:56: WARNING: Inline literal start-string without end-string.
/var/jenkins_home/workspace/yt_docs_new/yt/visualization/plot_modifications.py:docstring of yt.visualization.plot_modifications.TimestampCallback:61: WARNING: Unexpected indentation.
/var/jenkins_home/workspace/yt_docs_new/yt/visualization/plot_modifications.py:docstring of yt.visualization.plot_modifications.TimestampCallback:58: WARNING: Inline literal start-string without end-string.

MISC

various stuff I wasn't able to fix yet.

/var/jenkins_home/workspace/yt_docs_new/yt/data_objects/derived_quantities.py:docstring of yt.data_objects.derived_quantities.AngularMomentumVector:27: WARNING: Inline strong start-string without end-string.
/var/jenkins_home/workspace/yt_docs_new/doc/source/examining/loading_data.rst:4: WARNING: Duplicate explicit target name: "adaptahop".
/var/jenkins_home/workspace/yt_docs_new/doc/source/reference/changelog.rst:: WARNING: Anonymous hyperlink mismatch: 1 references but 0 targets.

[neutrinoceros]

Just reporting that the number of warnings seems to be increasing again already. This is expected since, for as long as we don't treat warning as failures, they are very hard to keep track of

build succeeded, 47 warnings.

[neutrinoceros]

not going to be 100% fixed in time for the release, but thanks to @cphyc and his work in #3394, we're closer than ever !
I'll move this to the 4.1 milestone

[neutrinoceros]

As of today we have 33 warnings, a handful of which look new

/var/jenkins_home/workspace/yt_docs_new/doc/source/reference/changelog.rst:563: WARNING: Title level inconsistent:

Testing and Infrastructure
""""""""""""""""""""""""""
/var/jenkins_home/workspace/yt_docs_new/doc/source/reference/changelog.rst:582: WARNING: Title level inconsistent:

CI related support
""""""""""""""""""
/var/jenkins_home/workspace/yt_docs_new/doc/source/reference/changelog.rst:606: WARNING: Title level inconsistent:

Other Infrastructure
""""""""""""""""""""
/var/jenkins_home/workspace/yt_docs_new/doc/source/developing/testing.rst:175: WARNING: Bullet list ends without a blank line; unexpected unindent.

[neutrinoceros]

update:

Looks to me that all of these would be solved by installing pyembree in the docs build. However, it seems to be only distributed via conda, and I don't think that conda is used here, so I don't know what to do.

There are now wheels available (only for Python 3.8) on PyPI. It could suffice.
edit: no, it doesn't, because that's not the actual problem here

I also want to revisit this and make sure we resolve all warnings we can before the 4.1 release.

[neutrinoceros]

I did what I could in #4108, the rest of the warnings are both out of my reach right now and non-critical.