DOC: Fix for building with sphinx 3

[takanori-pskq]

Related #16217
The warnings has decreased, but some warnings remain, and the generated document is still broken.

[charris]

.. c:enumerator:: seems to cause problems.

[takanori-pskq]

.. c:enumerator is a new feature in sphinx version 3, so I think this is the cause of failures with version 2.

[eric-wieser]

Could maybe keep the argument by using :c:expr: here

[takanori-pskq]

Using :c:expr:, this raises a warning: WARNING: c:identifier reference target not found: iter. I think this reference should be removed (``NpyIter_IterationNeedsAPI(iter)``).

[takanori-pskq]

Searching doesn't work. Maybe the cause is incompatibility of conf.py between version 2 and 3. (sphinx outputs no warning about it...?)

[rossbar]

There were a couple things that stood out to me from taking a quick look at this (I haven't made it all the way through yet):

1. It seems that there are a lot of changes that fit the pattern of :c:var: -> :c:macro:. In these cases the macros don't have arguments, which according to the sphinx docs is supported in sphinx 2.X. If these work as expected, they could potentially be moved to DOC: Remove links for C codes #16896 so that they can be incorporated sooner.
2. Sphinx 3 adds the :c:macro: name (arglist) pattern. This means that many of the things that are currently defined using the .. :c:function: directive can be switched over. Was there a reason you decided to stick with the .. :c:function: approach instead?

[mattip]

There are now merge conflicts here

[mattip]

Now there are warnings:

WARNING: Unknown directive type "c:enumerator"
WARNING: Unknown interpreted text role "c:expr"

[takanori-pskq]

The cause of these warnings is that we use sphinx 2. I fixed doc_requirements.txt. Now other warnings are raised:

WARNING: autodoc: failed to import function 'add' from module 'char'; the following exception was raised:
No module named 'char'
WARNING: autodoc: failed to import function 'array' from module 'char'; the following exception was raised:
No module named 'char'
WARNING: autodoc: failed to import function 'asarray' from module 'char'; the following exception was raised:
No module named 'char'
...

[mattip]

I still see the same warnings in the circleci : build job. Also you need to rebase or merge from master to fix the other bulid failures.

[rossbar]

The cause of these warnings is that we use sphinx 2. I fixed doc_requirements.txt. Now other warnings are raised:

This transition (from sphinx 2->3) seems like it will be tricky for this reason, since the doc builds are not going to be compatible between 2 & 3. I guess in this case we'd have to ignore the doc-build CI and run tests locally, or update the CI config as part of the PR (not sure if this change would get picked up though).

[mattip]

@takanori-pskq will you be continuing with this?

[mattip]

I think we should break this into two PRs: one to do the absolute minimum needed to get sphinx 3.2 to work, and another to update our C roles to a more modern sphinx. Note that sphinx 3.2 has a new c_allow_pre_v3 option to revert some of the breaking formatting changes.

[takanori-pskq]

c_allow_pre_v3 option raises warnings:

WARNING: RemovedInSphinx50Warning: Pre-v3 C type role ':c:type:`PyArrayObject *`' converted to ':c:expr:`PyArrayObject *`'.

And the warnings mentioned above (No module named 'char') remain.

[mattip]

I think you need to add c_warn_on_allowed_pre_v3=False as well

[eric-wieser]

This page has become monstrous due to the exclude-members issue: https://16376-908607-gh.circle-artifacts.com/0/doc/build/html/reference/arrays.scalars.html

[takanori-pskq]

Fixed the issue caused by exclude-members. I think this is not a good way, but I don't know the right way to fix.

.. autoclass:: numpy.generic
   :members: all
   :exclude-members: all

here all doesn't mean "all the members", but "one of the methods numpy.generic.all".

[eric-wieser]

Nice hack - although I don't like the use of all as that's confusing to the reader. My suggestion would be either:

• __init__, since that's guaranteed to be there
• this_member_does_not_exist, if sphinx doesn't get upset by it

[takanori-pskq]

__init__ seems to be better. Specifying a member that doesn't exist raises another warning.

[waveform80]

Fixed the issue caused by exclude-members. I think this is not a good way, but I don't know the right way to fix.

Theoretically, the "right" way to fix this is :no-members: as the sphinx autodoc documentation (very obscurely) suggests:

You can use a negated form, 'no-flag', as an option of autodoc directive, to disable it temporarily...

However, having tried it in this circumstance, it doesn't appear to work (I could swear it worked in earlier versions but I haven't had time to dig into this). In any case, you've a neat hack for working around it.

[eric-wieser]

This is looking really good now, thanks! I think my only remaining nit is :c:type: vs :c:expr.

Edit: Agreed to deal with that in a later PR, #16370 (comment)

[eric-wieser]

Note the -n build is emitting:

build finished with problems, 655 warnings.

Which is almost two times worse than it was before.

[takanori-pskq]

I found that there weren't many changes, so I fixed in this PR.

[eric-wieser]

The full set of warnings:

reference/arrays.classes.rst:514: WARNING: py:mod reference target not found: numpy.rec
reference/arrays.dtypes.rst:164: WARNING: py:class reference target not found: character
reference/arrays.dtypes.rst:164: WARNING: py:class reference target not found: string
reference/arrays.dtypes.rst:188: WARNING: py:class reference target not found: buffer
reference/arrays.dtypes.rst:304: WARNING: py:obj reference target not found: numpy.sctypeDict
reference/arrays.interface.rst:174: WARNING: py:class reference target not found: buffer
reference/arrays.ndarray.rst:4: WARNING: py:class reference target not found: ndarray
reference/arrays.ndarray.rst:24: WARNING: py:class reference target not found: buffer
reference/arrays.nditer.cython.rst:4: WARNING: py:class reference target not found: nditer
reference/c-api/array.rst:23: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:47: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:135: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:154: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:246: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:246: WARNING: c:identifier reference target not found: PyTypeObject
reference/c-api/array.rst:246: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:269: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:283: WARNING: c:identifier reference target not found: PyObject
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reference/c-api/array.rst:865: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:1025: WARNING: c:data reference target not found: NPY_LITTLE
reference/c-api/array.rst:1025: WARNING: c:data reference target not found: NPY_BIG
reference/c-api/array.rst:1025: WARNING: c:data reference target not found: NPY_NATIVE
reference/c-api/array.rst:1025: WARNING: c:data reference target not found: NPY_IGNORE
reference/c-api/array.rst:1025: WARNING: c:data reference target not found: NPY_LITTLE
reference/c-api/array.rst:1025: WARNING: c:data reference target not found: NPY_NATIVE
reference/c-api/array.rst:1042: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:1049: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:1070: WARNING: c:identifier reference target not found: PyArray_VectorUnaryFunc
reference/c-api/array.rst:1187: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:1198: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:1231: WARNING: c:identifier reference target not found: PyObject
reference/c-api/array.rst:1202: WARNING: c:data reference target not found: NPY_ITER_COMMON_DTYPE
reference/c-api/array.rst:1288: WARNING: c:identifier reference target not found: PyArray_VectorUnaryFunc
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[eric-wieser]

The WARNING: c:identifier reference target not found: PyObject errors account for 284 of the total errors, so we probably don't need to worry too much about the increase.

The error is strange, because the Python intersphinx contains

c:type
	PyObject                                 c-api/structures.html#c.PyObject

[takanori-pskq]

.. c:function:: func()

    description

    .. c:macro:: p
    .. c:macro:: q

Here, p and q seems not to work as global link targets in sphinx 3 (work in sphinx 2), so we need to dedent. This is another cause of increasing warnings.

[charris]

Is this ready now?

[takanori-pskq]

Yes, it is. I don't know how to remove the "WIP" label.

[rossbar]

FWIW I'm +1 on this. It seems like the sticking points (e.g. the increased warnings) shouldn't be blockers and could be dealt with in follow-up PRs, and getting the docs building on sphinx 3 is IMO worth the hiccups. It might be worth creating an issue for the :members:/:exclude-members: hack so that we can clean that up when a working solution (hopefully :no-members:) is available.

There's a lot of nice work in here, thanks @takanori-pskq!

[mattip]

Thanks @takanori-pskq. Hopefully there will not be much fallout from the transition.