DOC: Fix for building with sphinx 3 #16370

takanori-pskq · 2020-05-25T16:00:40Z

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

charris · 2020-05-25T17:27:59Z

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

takanori-pskq · 2020-05-26T01:54:48Z

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

doc/source/reference/c-api/array.rst

eric-wieser · 2020-05-26T08:18:43Z

doc/source/reference/c-api/iterator.rst

@@ -370,7 +370,7 @@ Construction and Destruction
            arrays or structured arrays containing an object type)
            may be accepted and used in the iterator.  If this flag
            is enabled, the caller must be sure to check whether
-            :c:func:`NpyIter_IterationNeedsAPI(iter)` is true, in which case


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

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)``).

doc/source/reference/c-api/types-and-structures.rst

doc/DISTUTILS.rst.txt

doc/source/reference/c-api/types-and-structures.rst

takanori-pskq · 2020-05-26T15:38:16Z

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):

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.
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?

doc/source/reference/c-api/array.rst

mattip · 2020-07-31T05:57:50Z

There are now merge conflicts here

mattip · 2020-08-02T08:24:29Z

Now there are warnings:

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

takanori-pskq · 2020-08-03T04:18:57Z

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 · 2020-08-03T04:39:50Z

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 · 2020-08-03T18:29:08Z

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 · 2020-09-16T09:36:08Z

@takanori-pskq will you be continuing with this?

mattip · 2020-09-16T10:37:28Z

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 · 2020-09-19T11:46:08Z

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 · 2020-09-19T13:00:59Z

I think you need to add c_warn_on_allowed_pre_v3=False as well

doc/source/reference/c-api/array.rst

doc/source/reference/c-api/dtype.rst

eric-wieser · 2020-10-14T13:51:40Z

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 · 2020-10-14T14:43:53Z

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 · 2020-10-14T18:07:24Z

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 · 2020-10-15T02:24:54Z

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

waveform80 · 2020-10-18T15:28:24Z

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.

doc/source/conf.py

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 · 2020-10-26T10:14:41Z

Note the -n build is emitting:

build finished with problems, 655 warnings.

Which is almost two times worse than it was before.

doc/source/conf.py

takanori-pskq · 2020-10-26T11:36:52Z

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

eric-wieser · 2020-10-26T11:47:15Z

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
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reference/c-api/array.rst:1025: WARNING: c:data reference target not found: NPY_LITTLE
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reference/c-api/array.rst:1025: WARNING: c:data reference target not found: NPY_IGNORE
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reference/c-api/array.rst:1025: WARNING: c:data reference target not found: NPY_NATIVE
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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
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user/c-info.how-to-extend.rst:434: WARNING: c:data reference target not found: NPY_ARRAY_INOUT_ARRAY
user/c-info.how-to-extend.rst:447: WARNING: c:data reference target not found: NPY_ARRAY_IN_ARRAY
user/c-info.how-to-extend.rst:454: WARNING: c:data reference target not found: NPY_ARRAY_OUT_ARRAY
user/c-info.how-to-extend.rst:470: WARNING: c:data reference target not found: NPY_ARRAY_INOUT_ARRAY

eric-wieser · 2020-10-26T11:49:47Z

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 · 2020-10-27T15:16:45Z

.. 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 · 2020-12-15T18:28:01Z

Is this ready now?

takanori-pskq · 2020-12-16T01:05:12Z

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 · 2020-12-16T07:29:52Z

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

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DOC: Remove links for C codes #16896

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DOC: Fix the declarations of C fuctions #16897

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DOC,BLD: Errors building docs with sphinx 3 #16217

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DOC: Remove directives for some constants #17559

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DOC: mark np.testing.dec functions as not recommended for future use #17566

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DOC: Fix typos #17571

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DOC: Fix the references for __array_*__ #17627

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C domain: References generated by types in function signatures don't use intersphinx sphinx-doc/sphinx#8341

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DOC: Fix for buildling with sphinx 3

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DOC: missing references when using -n in sphinx-build #13114

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