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

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mattip opened this issue Mar 13, 2019 · 39 comments · Fixed by #16300 or #23278
Open

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

mattip opened this issue Mar 13, 2019 · 39 comments · Fixed by #16300 or #23278

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@mattip
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mattip commented Mar 13, 2019

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.

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

@mattip
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mattip commented Mar 13, 2019

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
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I will like to contribute to this

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

@mattip
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mattip commented Apr 7, 2019

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.

@charris 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
@mattip
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mattip commented Jun 10, 2019

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

@rgommers
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rgommers commented May 4, 2020

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

@rossbar
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rossbar commented May 5, 2020

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
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  • numpy/doc/source/user/basics.io.genfromtxt.rst:38: WARNING: py:class reference target not found: bz2
  • numpy/doc/source/user/basics.io.genfromtxt.rst:38: WARNING: py:class reference target not found: gzip
  • numpy/doc/source/user/basics.io.genfromtxt.rst:38: WARNING: py:class reference target not found: bzip2
  • numpy/doc/source/user/basics.io.genfromtxt.rst:230: WARNING: py:class reference target not found: numpy.lib._iotools.StringConverter
  • numpy/doc/source/user/basics.io.genfromtxt.rst:360: WARNING: py:class reference target not found: datetime
  • numpy/doc/source/user/basics.io.genfromtxt.rst:430: WARNING: py:func reference target not found: nummpy.genfromtxt
  • numpy/doc/source/user/basics.io.genfromtxt.rst:517: WARNING: py:mod reference target not found: numpy.lib.io
  • numpy/doc/source/user/basics.io.genfromtxt.rst:525: WARNING: py:func reference target not found: numpy.recfromtxt
  • numpy/doc/source/user/basics.io.genfromtxt.rst:523: WARNING: py:class reference target not found: numpy.ma.MaskedRecords
  • numpy/doc/source/user/basics.io.genfromtxt.rst:527: WARNING: py:func reference target not found: numpy.recfromcsv
  • numpy/doc/source/user/basics.io.genfromtxt.rst:528: WARNING: py:func reference target not found: numpy.recfromtxt
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:127: WARNING: py:class reference target not found: numpy.object
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:281: WARNING: py:class reference target not found: numpy.void
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:530: WARNING: py:func reference target not found: ndarray.item
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:541: WARNING: py:class reference target not found: numpy.object
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:571: WARNING: py:mod reference target not found: numpy.rec
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:578: WARNING: py:func reference target not found: numpy.rec.array
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:594: WARNING: py:func reference target not found: numpy.rec.array
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:601: WARNING: py:mod reference target not found: numpy.rec
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:613: WARNING: py:class reference target not found: np.recarray
  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:613: WARNING: py:class reference target not found: np.record
  • 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
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rgommers commented May 5, 2020

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

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

@bsipocz
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bsipocz commented Apr 28, 2023

Pretty sure this would at least be very very difficult; it's sphinx that does the linking and AFAIK sphinx doesn't create targets for every function/method/class parameter.

I recall that Ross had a workaround in mind, and certainly showed me once that this is a bug rather than a feature. Either case, I would love if we could get to the bottom of it with a solution during the summit!

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rossbar commented Apr 28, 2023

Yeah I still strongly advocate for fixing this upstream in numpydoc - that way, the fix will apply to all libraries that use the numpydoc extension for their docstrings. As I've proposed elsewhere, I think there's a relatively straightforward path to try. It looks something like this:

  • Add a configuration param to numpydoc to allow users to select the default parameter role. For starters, this could be something like :emph: to resolve the nit-picky links issue.
  • Add code to the numpydoc parser to check for words enclosed in single-backticks in the summary, notes, parameter descriptions, etc. Compare these instances with the set of parameters, and replace any matches with the configured default role.

If I were to attempt solving this problem, this is where I'd start!

F3eQnxN3RriK added a commit to F3eQnxN3RriK/numpy that referenced this issue Jun 12, 2023
F3eQnxN3RriK added a commit to F3eQnxN3RriK/numpy that referenced this issue Jun 13, 2023
Corrected `lib.index_tricks.RClass` to `r_` instead of adding docstring of `RClass`.
Reducing 2 warnings (numpygh-13114).
seberg pushed a commit that referenced this issue Jun 13, 2023
Reducing 3 warnings (ref: gh-13114)


Co-authored-by: Matti Picus <matti.picus@gmail.com>
@mattip mattip removed the sprintable Issue fits the time-frame and setting of a sprint label Sep 20, 2023
F3eQnxN3RriK added a commit to F3eQnxN3RriK/numpy that referenced this issue Feb 7, 2024
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).

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F3eQnxN3RriK added a commit to F3eQnxN3RriK/numpy that referenced this issue Feb 7, 2024
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).

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rossbar pushed a commit that referenced this issue Feb 7, 2024
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).

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F3eQnxN3RriK added a commit to F3eQnxN3RriK/numpy that referenced this issue Feb 15, 2024
ref: numpygh-13114

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F3eQnxN3RriK added a commit to F3eQnxN3RriK/numpy that referenced this issue Feb 18, 2024
ref: numpygh-13114

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F3eQnxN3RriK added a commit to F3eQnxN3RriK/numpy that referenced this issue Mar 5, 2024
ref: numpygh-13114

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@mattip
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mattip commented Mar 6, 2024

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.

F3eQnxN3RriK added a commit to F3eQnxN3RriK/numpy that referenced this issue Mar 6, 2024
Fixed the first one in the list at numpy#13114 (comment).

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@mattip
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mattip commented Mar 6, 2024

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

F3eQnxN3RriK added a commit to F3eQnxN3RriK/numpy that referenced this issue Mar 9, 2024
Set module of ``MaskedArray`` to ``numpy.ma`` because
``numpy.ma.core.MaskedArray`` is an internal alias not documented.

ref: numpygh-13114

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charris pushed a commit to charris/numpy that referenced this issue Mar 9, 2024
Set module of ``MaskedArray`` to ``numpy.ma`` because
``numpy.ma.core.MaskedArray`` is an internal alias not documented.

ref: numpygh-13114

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