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

mattip · 2019-03-13T20:46:53Z

Started in #13104, turned into a tracking issue here.

Turning on -n in sphinx-build results in over 1000 warnings about bad references in docs. Trying to break these down with various grep statements, it seems about 200 are from numpy.ma, about 150 from polynomial and about 150 from c:type. That is under half of the WARNINGS.

~~My workflow is to cd to the doc directory, modify the ALLSPHINXOPTS in the Makefile and add -n`~~, My workflow is to set an environment variable SPHINXOPTS='-n' then run

(cd ..; pip install .); make clean; make html 2>&1 |tee /tmp/build.txt
less /tmp/build.txt

and look for the most common lines. Unfortunately this takes quite a while.

Anyone who wishes to contribute can issue PRs, preferably in chunks that address one class of failure. #13104 gives an idea of the changes needed.

The text was updated successfully, but these errors were encountered:

devayanipowar · 2019-03-13T21:21:21Z

I would like to contribute to this , I am just confused about what exactly to look upon

mattip · 2019-03-13T21:37:04Z

did you try to follow the steps above? Then you should look at the lines of /tmp/build.txt that have the WARNING in them

Jenniline · 2019-03-14T01:07:33Z

I will like to contribute to this

nicholas-castro · 2019-03-22T16:04:50Z

Hi, I'm working on this for the warnings that are generated for functions in the polynomial submodule. This is my first time working with Sphinx, so I have a rather basic question -- which docstring should I edit? Take, for example, the following error:

/usr/lib/python3.7/site-packages/numpy/polynomial/chebyshev.py:docstring of numpy.polynomial.chebyshev.chebdiv:29: WARNING: py:obj reference target not found: chemulx

which is due to a typo (should be chebmulx). The file at /usr/lib/python3.7/site-packages/numpy/polynomial/chebyshev.py is read-only, so I cannot save changes. However, if I edit my local copy of the repository in numpy/polynomial/chebyshev.py the changes don't seem to be reflected when I re-build the docs. If you could point me on the right path I'd be really grateful, sorry for the basic question.

parulagg27 · 2019-04-06T19:35:06Z

I'd also like to work on this issue and have the same question as mentioned by @nicholas-castro. Please kindly guide, @mattip

mattip · 2019-04-07T06:28:44Z

You need to re-install numpy into the python that is building the documentation, so that sphinx can pick up the changes. That is why there is a pip install . in what I wrote above.

@parulagg27 please coordinate with @nicholas-castro so that your work does not overlap.

mattip · 2019-06-10T08:30:57Z

Note that it is sufficient to set an environment variable SPHINXOPTS='-n' and then generate documentation, no need to edit the Makefile anymore.

rgommers · 2020-05-04T10:20:38Z

This is probably not fixed completely. It would be good if someone could try and paste the current status here.

rossbar · 2020-05-05T04:40:15Z

Here's the current status (generated from deb7943 on 5/4/20 using @mattip's workflow from the first comment):

Summary: 792 total warnings
* ~90 from numpy.ma docstrings
* ~120 from numpy.polynomial docstrings

Full log of link warnings

numpy/doc/sphinxext/doc/example.py:docstring of doc.example.foo:58: WARNING: py:obj reference target not found: otherfunc
numpy/doc/sphinxext/doc/example.py:docstring of doc.example.foo:61: WARNING: py:obj reference target not found: newfunc
numpy/doc/sphinxext/doc/example.py:docstring of doc.example.foo:63: WARNING: py:obj reference target not found: thirdfunc
numpy/doc/sphinxext/doc/example.py:docstring of doc.example.foo:63: WARNING: py:obj reference target not found: fourthfunc
numpy/doc/sphinxext/doc/example.py:docstring of doc.example.foo:63: WARNING: py:obj reference target not found: fifthfunc
numpy/doc/source/f2py/distutils.rst:29: WARNING: py:class reference target not found: Extension
numpy/doc/source/f2py/distutils.rst:40: WARNING: py:class reference target not found: Extension
numpy/doc/source/reference/arrays.classes.rst:481: WARNING: py:obj reference target not found: object_
numpy/doc/source/reference/arrays.classes.rst:481: WARNING: py:obj reference target not found: string_
numpy/doc/source/reference/arrays.classes.rst:481: WARNING: py:obj reference target not found: unicode_
numpy/doc/source/reference/arrays.classes.rst:487: WARNING: py:class reference target not found: string_
numpy/doc/source/reference/arrays.classes.rst:487: WARNING: py:class reference target not found: unicode_
numpy/doc/source/reference/arrays.classes.rst:487: WARNING: py:class reference target not found: unicode
numpy/doc/source/reference/arrays.classes.rst:515: WARNING: py:mod reference target not found: numpy.rec
numpy/doc/source/reference/arrays.dtypes.rst:44: WARNING: py:class reference target not found: void
numpy/doc/source/reference/arrays.dtypes.rst:81: WARNING: py:class reference target not found: int32
numpy/doc/source/reference/arrays.dtypes.rst:136: WARNING: py:class reference target not found: float_
numpy/doc/source/reference/arrays.dtypes.rst:147: WARNING: py:obj reference target not found: flexible
numpy/doc/source/reference/arrays.dtypes.rst:172: WARNING: py:class reference target not found: number
numpy/doc/source/reference/arrays.dtypes.rst:172: WARNING: py:class reference target not found: inexact
numpy/doc/source/reference/arrays.dtypes.rst:172: WARNING: py:class reference target not found: floating
numpy/doc/source/reference/arrays.dtypes.rst:173: WARNING: py:class reference target not found: complexfloating
numpy/doc/source/reference/arrays.dtypes.rst:173: WARNING: py:class reference target not found: cfloat
numpy/doc/source/reference/arrays.dtypes.rst:174: WARNING: py:class reference target not found: integer
numpy/doc/source/reference/arrays.dtypes.rst:174: WARNING: py:class reference target not found: signedinteger
numpy/doc/source/reference/arrays.dtypes.rst:174: WARNING: py:class reference target not found: int_
numpy/doc/source/reference/arrays.dtypes.rst:175: WARNING: py:class reference target not found: unsignedinteger
numpy/doc/source/reference/arrays.dtypes.rst:175: WARNING: py:class reference target not found: uint
numpy/doc/source/reference/arrays.dtypes.rst:176: WARNING: py:class reference target not found: character
numpy/doc/source/reference/arrays.dtypes.rst:176: WARNING: py:class reference target not found: string
numpy/doc/source/reference/arrays.dtypes.rst:177: WARNING: py:class reference target not found: flexible
numpy/doc/source/reference/arrays.dtypes.rst:177: WARNING: py:class reference target not found: void
numpy/doc/source/reference/arrays.dtypes.rst:186: WARNING: py:class reference target not found: int_
numpy/doc/source/reference/arrays.dtypes.rst:187: WARNING: py:class reference target not found: bool_
numpy/doc/source/reference/arrays.dtypes.rst:188: WARNING: py:class reference target not found: float_
numpy/doc/source/reference/arrays.dtypes.rst:189: WARNING: py:class reference target not found: cfloat
numpy/doc/source/reference/arrays.dtypes.rst:190: WARNING: py:class reference target not found: bytes_
numpy/doc/source/reference/arrays.dtypes.rst:191: WARNING: py:class reference target not found: str_
numpy/doc/source/reference/arrays.dtypes.rst:192: WARNING: py:class reference target not found: buffer
numpy/doc/source/reference/arrays.dtypes.rst:192: WARNING: py:class reference target not found: void
numpy/doc/source/reference/arrays.dtypes.rst:193: WARNING: py:class reference target not found: object_
numpy/doc/source/reference/arrays.dtypes.rst:259: WARNING: py:class reference target not found: void
numpy/doc/source/reference/arrays.dtypes.rst:314: WARNING: py:obj reference target not found: numpy.sctypeDict
numpy/doc/source/reference/arrays.dtypes.rst:404: WARNING: py:class reference target not found: string
numpy/doc/source/reference/arrays.dtypes.rst:404: WARNING: py:class reference target not found: unicode
numpy/doc/source/reference/arrays.indexing.rst:34: WARNING: py:const reference target not found: Ellipsis
numpy/doc/source/reference/arrays.indexing.rst:43: WARNING: py:const reference target not found: Ellipsis
numpy/doc/source/reference/arrays.indexing.rst:132: WARNING: py:const reference target not found: Ellipsis
numpy/doc/source/reference/arrays.indexing.rst:333: WARNING: py:const reference target not found: Ellipsis
numpy/doc/source/reference/arrays.indexing.rst:349: WARNING: py:class reference target not found: intp
numpy/doc/source/reference/arrays.indexing.rst:375: WARNING: py:const reference target not found: True
numpy/doc/source/reference/arrays.indexing.rst:383: WARNING: py:const reference target not found: True
numpy/doc/source/reference/arrays.indexing.rst:383: WARNING: py:const reference target not found: True
numpy/doc/source/reference/arrays.indexing.rst:383: WARNING: py:const reference target not found: False
numpy/doc/source/reference/arrays.interface.rst:64: WARNING: c:data reference target not found: Py_LONG_LONG
numpy/doc/source/reference/arrays.interface.rst:152: WARNING: py:const reference target not found: int
numpy/doc/source/reference/arrays.interface.rst:152: WARNING: py:const reference target not found: long
numpy/doc/source/reference/arrays.interface.rst:152: WARNING: c:type reference target not found: Py_LONG_LONG
numpy/doc/source/reference/arrays.interface.rst:181: WARNING: py:class reference target not found: buffer
numpy/doc/source/reference/arrays.interface.rst:202: WARNING: c:data reference target not found: voidptr
numpy/doc/source/reference/arrays.interface.rst:202: WARNING: c:type reference target not found: PyCObject
numpy/doc/source/reference/arrays.interface.rst:202: WARNING: py:obj reference target not found: array_struct
numpy/doc/source/reference/arrays.interface.rst:232: WARNING: py:const reference target not found: CONTIGUOUS
numpy/doc/source/reference/arrays.interface.rst:232: WARNING: py:const reference target not found: FORTRAN
numpy/doc/source/reference/arrays.interface.rst:232: WARNING: py:const reference target not found: ALIGNED
numpy/doc/source/reference/arrays.interface.rst:232: WARNING: py:const reference target not found: NOTSWAPPED
numpy/doc/source/reference/arrays.interface.rst:232: WARNING: py:const reference target not found: WRITEABLE
numpy/doc/source/reference/arrays.interface.rst:232: WARNING: py:const reference target not found: ARR_HAS_DESCR
numpy/doc/source/reference/arrays.interface.rst:243: WARNING: c:type reference target not found: PyCObject
numpy/doc/source/reference/arrays.interface.rst:243: WARNING: c:type reference target not found: PyCObject
numpy/doc/source/reference/arrays.interface.rst:243: WARNING: c:type reference target not found: PyCObject_FromVoidPtrAndDesc
numpy/doc/source/reference/arrays.ndarray.rst:4: WARNING: py:class reference target not found: ndarray
numpy/doc/source/reference/arrays.ndarray.rst:24: WARNING: py:class reference target not found: buffer
numpy/doc/source/reference/arrays.ndarray.rst:265: WARNING: py:obj reference target not found: array_struct
numpy/doc/source/reference/arrays.ndarray.rst:472: WARNING: py:func reference target not found: bool
numpy/doc/source/reference/arrays.ndarray.rst:607: WARNING: py:func reference target not found: int
numpy/doc/source/reference/arrays.ndarray.rst:607: WARNING: py:func reference target not found: float
numpy/doc/source/reference/arrays.ndarray.rst:607: WARNING: py:func reference target not found: complex
numpy/doc/source/reference/arrays.nditer.cython.rst:4: WARNING: py:class reference target not found: nditer
numpy/doc/source/reference/arrays.scalars.rst:25: WARNING: py:const reference target not found: True
numpy/doc/source/reference/arrays.scalars.rst:25: WARNING: py:const reference target not found: True
numpy/doc/source/reference/arrays.scalars.rst:25: WARNING: py:const reference target not found: isinstance(val, np.flexible)
numpy/doc/source/reference/arrays.scalars.rst:25: WARNING: py:class reference target not found: string
numpy/doc/source/reference/arrays.scalars.rst:25: WARNING: py:class reference target not found: unicode
numpy/doc/source/reference/arrays.scalars.rst:25: WARNING: py:class reference target not found: void
numpy/doc/source/reference/arrays.scalars.rst:38: WARNING: py:class reference target not found: intp
numpy/doc/source/reference/arrays.scalars.rst:38: WARNING: py:class reference target not found: uintp
numpy/doc/source/reference/arrays.scalars.rst:54: WARNING: py:class reference target not found: int8
numpy/doc/source/reference/arrays.scalars.rst:54: WARNING: py:class reference target not found: float64
numpy/doc/source/reference/arrays.scalars.rst:54: WARNING: py:class reference target not found: complex128
numpy/doc/source/reference/arrays.scalars.rst:54: WARNING: py:class reference target not found: intp
numpy/doc/source/reference/arrays.scalars.rst:54: WARNING: py:class reference target not found: uintp
numpy/doc/source/reference/arrays.scalars.rst:72: WARNING: py:class reference target not found: int_
numpy/doc/source/reference/arrays.scalars.rst:72: WARNING: py:class reference target not found: IntType
numpy/doc/source/reference/arrays.scalars.rst:73: WARNING: py:class reference target not found: float_
numpy/doc/source/reference/arrays.scalars.rst:73: WARNING: py:class reference target not found: FloatType
numpy/doc/source/reference/arrays.scalars.rst:74: WARNING: py:class reference target not found: complex_
numpy/doc/source/reference/arrays.scalars.rst:74: WARNING: py:class reference target not found: ComplexType
numpy/doc/source/reference/arrays.scalars.rst:75: WARNING: py:class reference target not found: bytes_
numpy/doc/source/reference/arrays.scalars.rst:75: WARNING: py:class reference target not found: BytesType
numpy/doc/source/reference/arrays.scalars.rst:76: WARNING: py:class reference target not found: unicode_
numpy/doc/source/reference/arrays.scalars.rst:76: WARNING: py:class reference target not found: UnicodeType
numpy/doc/source/reference/arrays.scalars.rst:78: WARNING: py:class reference target not found: bool_
numpy/doc/source/reference/arrays.scalars.rst:78: WARNING: py:class reference target not found: BooleanType
numpy/doc/source/reference/arrays.scalars.rst:78: WARNING: py:class reference target not found: BooleanType
numpy/doc/source/reference/arrays.scalars.rst:86: WARNING: py:class reference target not found: bool_
numpy/doc/source/reference/arrays.scalars.rst:86: WARNING: py:class reference target not found: int_
numpy/doc/source/reference/arrays.scalars.rst:86: WARNING: py:class reference target not found: bool_
numpy/doc/source/reference/arrays.scalars.rst:93: WARNING: py:class reference target not found: int_
numpy/doc/source/reference/arrays.scalars.rst:97: WARNING: py:class reference target not found: float_
numpy/doc/source/reference/arrays.scalars.rst:110: WARNING: py:class reference target not found: bool_
numpy/doc/source/reference/arrays.scalars.rst:111: WARNING: py:class reference target not found: bool8
numpy/doc/source/reference/arrays.scalars.rst:117: WARNING: py:class reference target not found: byte
numpy/doc/source/reference/arrays.scalars.rst:118: WARNING: py:class reference target not found: short
numpy/doc/source/reference/arrays.scalars.rst:119: WARNING: py:class reference target not found: intc
numpy/doc/source/reference/arrays.scalars.rst:120: WARNING: py:class reference target not found: int_
numpy/doc/source/reference/arrays.scalars.rst:121: WARNING: py:class reference target not found: longlong
numpy/doc/source/reference/arrays.scalars.rst:122: WARNING: py:class reference target not found: intp
numpy/doc/source/reference/arrays.scalars.rst:123: WARNING: py:class reference target not found: int8
numpy/doc/source/reference/arrays.scalars.rst:124: WARNING: py:class reference target not found: int16
numpy/doc/source/reference/arrays.scalars.rst:125: WARNING: py:class reference target not found: int32
numpy/doc/source/reference/arrays.scalars.rst:126: WARNING: py:class reference target not found: int64
numpy/doc/source/reference/arrays.scalars.rst:132: WARNING: py:class reference target not found: ubyte
numpy/doc/source/reference/arrays.scalars.rst:133: WARNING: py:class reference target not found: ushort
numpy/doc/source/reference/arrays.scalars.rst:134: WARNING: py:class reference target not found: uintc
numpy/doc/source/reference/arrays.scalars.rst:135: WARNING: py:class reference target not found: uint
numpy/doc/source/reference/arrays.scalars.rst:136: WARNING: py:class reference target not found: ulonglong
numpy/doc/source/reference/arrays.scalars.rst:137: WARNING: py:class reference target not found: uintp
numpy/doc/source/reference/arrays.scalars.rst:138: WARNING: py:class reference target not found: uint8
numpy/doc/source/reference/arrays.scalars.rst:139: WARNING: py:class reference target not found: uint16
numpy/doc/source/reference/arrays.scalars.rst:140: WARNING: py:class reference target not found: uint32
numpy/doc/source/reference/arrays.scalars.rst:141: WARNING: py:class reference target not found: uint64
numpy/doc/source/reference/arrays.scalars.rst:147: WARNING: py:class reference target not found: half
numpy/doc/source/reference/arrays.scalars.rst:148: WARNING: py:class reference target not found: single
numpy/doc/source/reference/arrays.scalars.rst:149: WARNING: py:class reference target not found: double
numpy/doc/source/reference/arrays.scalars.rst:150: WARNING: py:class reference target not found: float_
numpy/doc/source/reference/arrays.scalars.rst:151: WARNING: py:class reference target not found: longfloat
numpy/doc/source/reference/arrays.scalars.rst:152: WARNING: py:class reference target not found: float16
numpy/doc/source/reference/arrays.scalars.rst:153: WARNING: py:class reference target not found: float32
numpy/doc/source/reference/arrays.scalars.rst:154: WARNING: py:class reference target not found: float64
numpy/doc/source/reference/arrays.scalars.rst:155: WARNING: py:class reference target not found: float96
numpy/doc/source/reference/arrays.scalars.rst:156: WARNING: py:class reference target not found: float128
numpy/doc/source/reference/arrays.scalars.rst:162: WARNING: py:class reference target not found: csingle
numpy/doc/source/reference/arrays.scalars.rst:163: WARNING: py:class reference target not found: complex_
numpy/doc/source/reference/arrays.scalars.rst:164: WARNING: py:class reference target not found: clongfloat
numpy/doc/source/reference/arrays.scalars.rst:165: WARNING: py:class reference target not found: complex64
numpy/doc/source/reference/arrays.scalars.rst:166: WARNING: py:class reference target not found: complex128
numpy/doc/source/reference/arrays.scalars.rst:167: WARNING: py:class reference target not found: complex192
numpy/doc/source/reference/arrays.scalars.rst:169: WARNING: py:class reference target not found: complex256
numpy/doc/source/reference/arrays.scalars.rst:176: WARNING: py:class reference target not found: object_
numpy/doc/source/reference/arrays.scalars.rst:180: WARNING: py:class reference target not found: object_
numpy/doc/source/reference/arrays.scalars.rst:186: WARNING: py:class reference target not found: object_
numpy/doc/source/reference/arrays.scalars.rst:186: WARNING: py:class reference target not found: object_
numpy/doc/source/reference/arrays.scalars.rst:200: WARNING: py:class reference target not found: bytes_
numpy/doc/source/reference/arrays.scalars.rst:201: WARNING: py:class reference target not found: unicode_
numpy/doc/source/reference/arrays.scalars.rst:202: WARNING: py:class reference target not found: void
numpy/doc/source/reference/arrays.scalars.rst:221: WARNING: py:obj reference target not found: array_priority
numpy/doc/source/reference/c-api/array.rst:607: WARNING: py:obj reference target not found: array_struct
numpy/doc/source/reference/c-api/array.rst:813: WARNING: c:type reference target not found: op
numpy/doc/source/reference/c-api/array.rst:813: WARNING: c:type reference target not found: dtype
numpy/doc/source/reference/c-api/array.rst:813: WARNING: c:type reference target not found: context
numpy/doc/source/reference/c-api/array.rst:813: WARNING: c:type reference target not found: out
numpy/doc/source/reference/c-api/array.rst:818: WARNING: c:type reference target not found: op
numpy/doc/source/reference/c-api/array.rst:822: WARNING: c:type reference target not found: op
numpy/doc/source/reference/c-api/array.rst:822: WARNING: c:type reference target not found: cls
numpy/doc/source/reference/c-api/array.rst:821: WARNING: c:data reference target not found: Py{cls}ArrType_Type
numpy/doc/source/reference/c-api/array.rst:828: WARNING: c:type reference target not found: op
numpy/doc/source/reference/c-api/array.rst:825: WARNING: c:data reference target not found: PyGenericArr_Type
numpy/doc/source/reference/c-api/array.rst:833: WARNING: c:type reference target not found: op
numpy/doc/source/reference/c-api/array.rst:838: WARNING: c:type reference target not found: op
numpy/doc/source/reference/c-api/array.rst:844: WARNING: c:type reference target not found: op
numpy/doc/source/reference/c-api/array.rst:841: WARNING: c:data reference target not found: PyGenericArr_Type
numpy/doc/source/reference/c-api/array.rst:852: WARNING: c:type reference target not found: op
numpy/doc/source/reference/c-api/array.rst:847: WARNING: c:data reference target not found: PyGenericArr_Type
numpy/doc/source/reference/c-api/array.rst:988: WARNING: c:type reference target not found: m
numpy/doc/source/reference/c-api/array.rst:993: WARNING: c:type reference target not found: m
numpy/doc/source/reference/c-api/array.rst:1002: WARNING: c:type reference target not found: Bool
numpy/doc/source/reference/c-api/array.rst:1008: WARNING: c:type reference target not found: Bool
numpy/doc/source/reference/c-api/array.rst:1013: WARNING: c:type reference target not found: Bool
numpy/doc/source/reference/c-api/array.rst:1023: WARNING: c:type reference target not found: byteorder
numpy/doc/source/reference/c-api/array.rst:1023: WARNING: c:type reference target not found: byteorder
numpy/doc/source/reference/c-api/array.rst:1016: WARNING: c:data reference target not found: NPY_LITTLE
numpy/doc/source/reference/c-api/array.rst:1016: WARNING: c:data reference target not found: NPY_BIG
numpy/doc/source/reference/c-api/array.rst:1016: WARNING: c:data reference target not found: NPY_NATIVE
numpy/doc/source/reference/c-api/array.rst:1016: WARNING: c:data reference target not found: NPY_IGNORE
numpy/doc/source/reference/c-api/array.rst:1016: WARNING: c:data reference target not found: NPY_LITTLE
numpy/doc/source/reference/c-api/array.rst:1016: WARNING: c:data reference target not found: NPY_NATIVE
numpy/doc/source/reference/c-api/array.rst:1061: WARNING: c:type reference target not found: PyArray_VectorUnaryFunc
numpy/doc/source/reference/c-api/array.rst:1165: WARNING: c:type reference target not found: arrs
numpy/doc/source/reference/c-api/array.rst:1165: WARNING: c:type reference target not found: dtypes
numpy/doc/source/reference/c-api/array.rst:1279: WARNING: c:type reference target not found: PyArray_VectorUnaryFunc
numpy/doc/source/reference/c-api/array.rst:1325: WARNING: c:func reference target not found: PyArray_DECREF
numpy/doc/source/reference/c-api/array.rst:1335: WARNING: c:func reference target not found: PyArray_SetWritebackIfCopyBase`
numpy/doc/source/reference/c-api/array.rst:1542: WARNING: c:type reference target not found: flags
numpy/doc/source/reference/c-api/array.rst:1660: WARNING: c:type reference target not found: Bool
numpy/doc/source/reference/c-api/array.rst:1941: WARNING: c:type reference target not found: NPY_SEARCHSIDE
numpy/doc/source/reference/c-api/array.rst:1933: WARNING: c:data reference target not found: NPY_SEARCHLEFT
numpy/doc/source/reference/c-api/array.rst:1933: WARNING: c:data reference target not found: NPY_SEARCHRIGHT
numpy/doc/source/reference/c-api/array.rst:1958: WARNING: c:type reference target not found: NPY_SELECTKIND
numpy/doc/source/reference/c-api/array.rst:1966: WARNING: c:type reference target not found: NPY_SELECTKIND
numpy/doc/source/reference/c-api/array.rst:2326: WARNING: c:type reference target not found: Bool
numpy/doc/source/reference/c-api/array.rst:2424: WARNING: c:type reference target not found: auxdata
numpy/doc/source/reference/c-api/array.rst:2429: WARNING: c:type reference target not found: auxdata
numpy/doc/source/reference/c-api/array.rst:2810: WARNING: c:data reference target not found: NPY_IGNORE
numpy/doc/source/reference/c-api/array.rst:2810: WARNING: c:data reference target not found: NPY_SWAP
numpy/doc/source/reference/c-api/array.rst:2810: WARNING: c:data reference target not found: NPY_NATIVE
numpy/doc/source/reference/c-api/array.rst:2810: WARNING: c:data reference target not found: NPY_LITTLE
numpy/doc/source/reference/c-api/array.rst:2810: WARNING: c:data reference target not found: NPY_BIG
numpy/doc/source/reference/c-api/array.rst:2940: WARNING: c:data reference target not found: NPY_BEHAVED_RO
numpy/doc/source/reference/c-api/array.rst:2967: WARNING: c:type reference target not found: Bool
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numpy/numpy/lib/recfunctions.py:docstring of numpy.lib.recfunctions.repack_fields:8: WARNING: py:obj reference target not found: np.dtype
numpy/numpy/lib/recfunctions.py:docstring of numpy.lib.recfunctions.structured_to_unstructured:21: WARNING: py:obj reference target not found: ndarray.astype
numpy/numpy/lib/recfunctions.py:docstring of numpy.lib.recfunctions.structured_to_unstructured:25: WARNING: py:obj reference target not found: ndarray.astype
numpy/numpy/lib/recfunctions.py:docstring of numpy.lib.recfunctions.unstructured_to_structured:29: WARNING: py:obj reference target not found: ndarray.astype
numpy/numpy/lib/recfunctions.py:docstring of numpy.lib.recfunctions.unstructured_to_structured:33: WARNING: py:obj reference target not found: ndarray.astype
numpy/doc/source/user/c-info.beyond-basics.rst:115: WARNING: c:func reference target not found: PyArray_Iter_GOTO1D
numpy/doc/source/user/c-info.beyond-basics.rst:162: WARNING: c:type reference target not found: PyArrayMultiObject *
numpy/doc/source/user/c-info.beyond-basics.rst:162: WARNING: c:func reference target not found: PyArray_MultiIter_SIZE
numpy/doc/source/user/c-info.beyond-basics.rst:264: WARNING: c:func reference target not found: PyArray_TypeNumFromName
numpy/doc/source/user/c-info.beyond-basics.rst:466: WARNING: c:func reference target not found: PyArray_FinalizeFunc
numpy/doc/source/user/quickstart.rst:773: WARNING: py:obj reference target not found: row_stack
numpy/doc/source/user/quickstart.rst:773: WARNING: py:obj reference target not found: row_stack

copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build finished with problems, 792 warnings.
make: *** [Makefile:179: html-build] Error 1

rgommers · 2020-05-05T09:13:35Z

Thanks @rossbar. Okay, there's still some low-hanging fruit here. Let's leave it as a "good first issue".

For clarity: the issue is that there are references (things with single backticks around them, i.e. `somename`) that do not reference another function or object that can be found.

There's a couple of types of solutions:

In some cases the intent was to typeset as code rather than a reference. This is done by adding double backticks. Example; `True` should be ``True`` (or simply without backticks).
In other cases, a reference is meant but it cannot be found. Example: the numpy.ma.argsort has a reference to lexsort in its See Also; there's no numpy.ma.lexsort so this means numpy.lexsort. On reflection, that link should be valid (as are many others), there may be something wrong with the lookup mechanism. IIRC the rules are that first the current scope is checked for a matching name, and then the next scope up. In SciPy this works correctly, in NumPy it does seem to - some .. currentmodule::'s set incorrectly perhaps?

tl;dr the "this is not a reference" is easy to fix, the other part requires knowledge of Sphinx and Numpydoc.

takanori-pskq · 2020-05-12T13:19:38Z

I would like to contribute to this issue. Is someone working on this now?

rgommers · 2020-05-12T13:24:03Z

@takanori-pskq I don't think so. Please dive in, help is very welcome!

Reducing 3 warnings (ref: numpygh-13114)

Corrected `lib.index_tricks.RClass` to `r_` instead of adding docstring of `RClass`. Reducing 2 warnings (numpygh-13114).

Reducing 3 warnings (ref: gh-13114) Co-authored-by: Matti Picus <matti.picus@gmail.com>

The python module ``distutils`` was removed in latest version (3.12), so the document of ``distutils`` does not exist. Reduced 4 reference warnings (see numpygh-13114). [skip cirrus] [skip azp] [skip actions]

The python module ``distutils`` was removed in latest version (3.12), so the document of ``distutils`` does not exist. Reduced 4 reference warnings (see gh-13114). [skip cirrus] [skip azp] [skip actions]

ref: numpygh-13114 [skip cirrus] [skip azp] [skip actions]

mattip · 2024-03-06T09:22:24Z

After #25939 we are down to 30 warnings, thanks to all who contributed fixes especially @F3eQnxN3RriK. The remaining warnings:

Parsing PyArrayDescr as a parameter type seems to fail here and in the other similar declarations (9 warnings)
FILE, size_t and PyHeapTypeObject are not valid refs (13 warnings)
something about missing docstrings in CPython's collections.abc.Mapping functions (4 warnings)
Missing numpy.ma.core.MaskedArray (3 warnings), has it moved?
A missing pandas.DataFrame.to_numpy reference (1 warning)

remaining warnings>

LANG=C sphinx-build -b html -WT --keep-going -d build/doctrees  -j2 -n source build/html 
Running Sphinx v7.2.6
2.0.dev0 2.0.0.dev0+git20240305.8d26d6c

...

/home/circleci/repo/doc/source/reference/c-api/array.rst:766: WARNING: Error in declarator or parameters

Invalid C declaration: Expecting "(" in parameters. [error at 13]
  The Metadata attached to a dtype, either ``NULL`` or a dictionary.
  -------------^
/home/circleci/repo/doc/source/reference/c-api/array.rst:769: WARNING: Invalid C declaration: Expected identifier in nested name. [error at 0]
  ``NULL`` or a list of structured field names attached to a dtype,
  ^
/home/circleci/repo/doc/source/reference/c-api/array.rst:769: WARNING: Error in declarator or parameters
Invalid C declaration: Expecting "(" in parameters. [error at 10]
  this list should not be mutated, NumPy may change the way fields are
  ----------^
/home/circleci/repo/doc/source/reference/c-api/array.rst:769: WARNING: Error in declarator or parameters
Invalid C declaration: Expecting "(" in parameters. [error at 10]
  stored in the future.
  ----------^
/home/circleci/repo/doc/source/reference/c-api/array.rst:774: WARNING: Invalid C declaration: Expected identifier in nested name. [error at 0]
  ``NULL``, ``None``, or a dict of structured dtype fields, this dict must
  ^
/home/circleci/repo/doc/source/reference/c-api/array.rst:774: WARNING: Error in declarator or parameters
Invalid C declaration: Expecting "(" in parameters. [error at 7]
  not be mutated, NumPy may change the way fields are stored in the future.
  -------^
/home/circleci/repo/doc/source/reference/c-api/array.rst:778: WARNING: Error in declarator or parameters
Invalid C declaration: Expected identifier in nested name. [error at 1]
  C-metadata object attached to a descriptor.  This accessor should not
  -^
/home/circleci/repo/doc/source/reference/c-api/array.rst:778: WARNING: Error in declarator or parameters
Invalid C declaration: Expecting "(" in parameters. [error at 10]
  be needed usually.  The C-Metadata field does provide access to the
  ----------^
/home/circleci/repo/doc/source/reference/c-api/array.rst:778: WARNING: Error in declarator or parameters
Invalid C declaration: Expected identifier in nested name. [error at 8]
  datetime/timedelta time unit information.
  --------^
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
/home/circleci/repo/doc/source/reference/c-api/array.rst:573: WARNING: c:identifier reference target not found: FILE
/home/circleci/repo/doc/source/reference/c-api/array.rst:2046: WARNING: c:identifier reference target not found: FILE
/home/circleci/repo/doc/source/reference/c-api/array.rst:3904: WARNING: c:identifier reference target not found: size_t
/home/circleci/repo/doc/source/reference/c-api/array.rst:3908: WARNING: c:identifier reference target not found: size_t
/home/circleci/repo/doc/source/reference/c-api/array.rst:3917: WARNING: c:identifier reference target not found: size_t
/home/circleci/repo/doc/source/reference/c-api/array.rst:3921: WARNING: c:identifier reference target not found: size_t
/home/circleci/repo/doc/source/reference/c-api/array.rst:3925: WARNING: c:identifier reference target not found: size_t
/home/circleci/repo/doc/source/reference/c-api/types-and-structures.rst:640: WARNING: c:identifier reference target not found: FILE
/home/circleci/repo/doc/source/reference/c-api/types-and-structures.rst:864: WARNING: c:identifier reference target not found: PyHeapTypeObject
/home/circleci/.pyenv/versions/3.11.4/lib/python3.11/collections/abc.py:docstring of collections.abc.Mapping.get:1: WARNING: py:class reference target not found: D[k] if k in D, else d.  d defaults to None.
/home/circleci/.pyenv/versions/3.11.4/lib/python3.11/collections/abc.py:docstring of collections.abc.Mapping.items:1: WARNING: py:class reference target not found: a set-like object providing a view on D's items
/home/circleci/.pyenv/versions/3.11.4/lib/python3.11/collections/abc.py:docstring of collections.abc.Mapping.keys:1: WARNING: py:class reference target not found: a set-like object providing a view on D's keys
/home/circleci/.pyenv/versions/3.11.4/lib/python3.11/collections/abc.py:docstring of collections.abc.Mapping.values:1: WARNING: py:class reference target not found: an object providing a view on D's values
<unknown>:1: WARNING: py:class reference target not found: numpy.ma.core.MaskedArray
/home/circleci/repo/doc/source/reference/maskedarray.generic.rst:106:<autosummary>:1: WARNING: py:class reference target not found: numpy.ma.core.MaskedArray
/home/circleci/repo/doc/source/reference/random/c-api.rst:174: WARNING: c:identifier reference target not found: size_t
/home/circleci/repo/doc/source/reference/random/c-api.rst:174: WARNING: c:identifier reference target not found: size_t
/home/circleci/repo/doc/source/reference/random/c-api.rst:176: WARNING: c:identifier reference target not found: size_t
/home/circleci/repo/doc/source/reference/random/c-api.rst:176: WARNING: c:identifier reference target not found: size_t
/home/circleci/repo/doc/source/reference/routines.ma.rst:36:<autosummary>:1: WARNING: py:class reference target not found: numpy.ma.core.MaskedArray
/home/circleci/repo/doc/source/user/how-to-io.rst:330: WARNING: py:meth reference target not found: pandas.DataFrame.to_numpy
writing output... [100%] release/1.23.2-notes .. user/whatisnumpy
generating indices... genindex done
writing additional pages... search done
copying images... [100%] ../build/plot_directive/user/quickstart-2.png
dumping search index in English (code: en)... done
dumping object inventory... done
build finished with problems, 30 warnings.

Fixed the first one in the list at numpy#13114 (comment). [skip cirrus] [skip azp] [skip actions]

mattip · 2024-03-06T12:02:02Z

Hmm, the 2.0 release notes have new warnings too:

new warnings

/home/circleci/repo/doc/source/release/2.0.0-notes.rst:798: WARNING: py:obj reference target not found: numpy.linalg.vecdot
/home/circleci/repo/doc/source/release/2.0.0-notes.rst:1211: WARNING: py:obj reference target not found: numpy.fft._helper
/home/circleci/repo/doc/source/release/2.0.0-notes.rst:1220: WARNING: py:obj reference target not found: numpy.linalg._linalg

Set module of ``MaskedArray`` to ``numpy.ma`` because ``numpy.ma.core.MaskedArray`` is an internal alias not documented. ref: numpygh-13114 [skip cirrus] [skip azp] [skip actions]

mattip · 2024-12-26T13:19:54Z

Closing, we now fail the doc build on warnings. Thanks to all who contributed to getting this long-standing issue fixed.

mattip added 04 - Documentation difficulty: Easy labels Mar 13, 2019

mattip mentioned this issue Mar 13, 2019

DOC: fix references in docs #13104

Merged

mattip changed the title ~~DOC: misssing referencese when using -n in sphinx-build~~ DOC: misssing references when using -n in sphinx-build Mar 21, 2019

mattip mentioned this issue Mar 21, 2019

DOC, BUILD: fail the devdoc build if there are warnings #13170

Merged

charris changed the title ~~DOC: misssing references when using -n in sphinx-build~~ DOC: missing references when using -n in sphinx-build Apr 7, 2019

tallamjr mentioned this issue Jun 6, 2019

runtests.py no longer builds on windows #13689

Closed

mattip mentioned this issue Jun 10, 2019

"Contributing to NumPy" links not rendering? #13740

Closed

kritisingh1 mentioned this issue Jul 19, 2019

DOC: Resolve bad references in Sphinx warnings #14064

Merged

mattip mentioned this issue Sep 25, 2019

DOC: Document the NPY_SCALARKIND values as C variables. #14576

Merged

mattip mentioned this issue Oct 15, 2019

Doc warnings #14699

Merged

takanori-pskq mentioned this issue May 19, 2020

DOC: Fix bad reference in numpy.ma #16300

Merged

takanori-pskq mentioned this issue Jul 3, 2020

DOC: Prepend ma. to references in numpy.ma #16736

Merged

koyuki7w added a commit to koyuki7w/numpy that referenced this issue Jun 12, 2023

DOC: Fix references to AxisError in docstrings

955f30b

Reducing 3 warnings (ref: numpygh-13114)

koyuki7w mentioned this issue Jun 12, 2023

DOC: Fix references to AxisError in docstrings #23918

Merged

koyuki7w added a commit to koyuki7w/numpy that referenced this issue Jun 13, 2023

DOC: Fix references to r_ in mr_class docstring

8324cf1

Corrected `lib.index_tricks.RClass` to `r_` instead of adding docstring of `RClass`. Reducing 2 warnings (numpygh-13114).

koyuki7w mentioned this issue Jun 13, 2023

DOC: Fix references to r_ in mr_class docstring #23927

Merged

seberg pushed a commit that referenced this issue Jun 13, 2023

DOC: Fix references to AxisError in docstrings (#23918)

9aca665

Reducing 3 warnings (ref: gh-13114) Co-authored-by: Matti Picus <matti.picus@gmail.com>

liang3zy22 mentioned this issue Jul 6, 2023

DOC: Fix warning for PyArray_MapIterNew. #24130

Merged

mattip removed the sprintable Issue fits the time-frame and setting of a sprint label Sep 20, 2023

mattip mentioned this issue Dec 27, 2023

DOC: Update a few interpreted text to verbatim/code. #25501

Merged

koyuki7w mentioned this issue Feb 7, 2024

DOC: Remove references to distutils in simd document #25783

Merged

koyuki7w added a commit to koyuki7w/numpy that referenced this issue Feb 15, 2024

DOC: Fix some reference warnings

80fdf5d

ref: numpygh-13114 [skip cirrus] [skip azp] [skip actions]

koyuki7w mentioned this issue Feb 15, 2024

DOC: Fix some reference warnings #25833

Merged

koyuki7w added a commit to koyuki7w/numpy that referenced this issue Feb 18, 2024

DOC: Fix some reference warnings

273f6aa

ref: numpygh-13114 [skip cirrus] [skip azp] [skip actions]

koyuki7w mentioned this issue Feb 18, 2024

DOC: Fix some reference warnings #25851

Merged

koyuki7w added a commit to koyuki7w/numpy that referenced this issue Mar 5, 2024

DOC: Add entries of npy_datetime and npy_timedelta

d83463c

ref: numpygh-13114 [skip cirrus] [skip azp] [skip actions]

koyuki7w mentioned this issue Mar 5, 2024

DOC: Add entries of npy_datetime and npy_timedelta #25939

Merged

koyuki7w added a commit to koyuki7w/numpy that referenced this issue Mar 6, 2024

DOC: Fix incorrect rst markups of c function directives

0170958

Fixed the first one in the list at numpy#13114 (comment). [skip cirrus] [skip azp] [skip actions]

koyuki7w mentioned this issue Mar 6, 2024

DOC: Fix incorrect rst markups of c function directives #25947

Merged

mattip mentioned this issue Mar 8, 2024

CI: fix last docbuild warnings #25964

Merged

koyuki7w mentioned this issue Mar 9, 2024

DOC: Fix module setting of MaskedArray #25972

Merged

This was referenced Mar 9, 2024

DOC: Backport gh-25971 and gh-25972 #25973

Merged

CI: fix last docbuild warnings #25983

Merged

mattip closed this as completed Dec 26, 2024

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

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