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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 · 31 comments · Fixed by #16300
Open

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

mattip opened this issue Mar 13, 2019 · 31 comments · Fixed by #16300
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04 - Documentation sprintable Issue fits the time-frame and setting of a sprint

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@mattip
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mattip commented Mar 13, 2019 •
edited

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.
@mattip mattip mentioned this issue Mar 13, 2019
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@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
@mattip mattip mentioned this issue Mar 21, 2019
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@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
@tallamjr tallamjr mentioned this issue Jun 6, 2019
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@mattip mattip mentioned this issue Jun 10, 2019
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@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.

@kritisingh1 kritisingh1 mentioned this issue Jul 19, 2019
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@mattip mattip mentioned this issue Sep 25, 2019
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@mattip mattip mentioned this issue Oct 15, 2019
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@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 •
edited by rgommers

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
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  • numpy/doc/source/release/1.17.0-notes.rst:178: WARNING: py:obj reference target not found: RandomState.logistic
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  • numpy/doc/source/release/1.5.0-notes.rst:38: WARNING: py:obj reference target not found: numpy.ComplexWarning
  • numpy/doc/source/user/basics.io.genfromtxt.rst:29: WARNING: py:meth reference target not found: read
  • numpy/doc/source/user/basics.io.genfromtxt.rst:38: WARNING: py:class reference target not found: gzip
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  • 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
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  • numpy/numpy/doc/structured_arrays.py:docstring of numpy.doc.structured_arrays:127: WARNING: py:class reference target not found: numpy.object
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  • numpy/doc/source/user/c-info.beyond-basics.rst:115: WARNING: c:func reference target not found: PyArray_Iter_GOTO1D
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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!

@takanori-pskq takanori-pskq mentioned this issue May 19, 2020
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@UtkarshRjn
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Hey, I am new to open source. Can I be assigned this project? Can someone guide me on how to get started?

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mattip commented Sep 30, 2021

PRs that reduce the number of warnings are welcome. Instructions for one workflow are at the top of the issue. Try to make some progress and ask if you get stuck.

@cmarmo cmarmo mentioned this issue Oct 19, 2021
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@SiddheshBangar
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Hello, I am new to open source, can I also be assigned to this project? and it would be great if some guidance can be provided about this issue and how to go forward with it. Thanks.

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mattip commented Nov 29, 2021

@SiddheshBangar we do not assign issues. PRs that reduce the number of warnings are welcome. Instructions for one workflow are at the top of the issue. Try to make some progress and ask if you get stuck.

@SiddheshBangar
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Sorry sir @mattip, I am just confused, to exactly what should I look upon, I tried figuring it out but still don't get it.

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Hi @SiddheshBangar, I would suggest you first build the documentation by following this guide; it will help you to see how we use Sphinx for our docs. Next, follow the workflow in the first comment and you'll see the warnings that should be fixed. See Ralf's comment for some insight into how to fix these warnings. Also, see the work done in gh-13104 for more guidance.

If you have problems re-creating the workflow, please let us know what you tried and what happened so that we can help you out!

@ChunkyGrumbler ChunkyGrumbler mentioned this issue Jan 2, 2022
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@jon-deng
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jon-deng commented Feb 2, 2022

Hi,

I wanted to make some small contributions to this and have picked out the errors:

docstring of numpy.arccos:46: WARNING: py:obj reference target not found: emath.arccos
docstring of numpy.arcsin:44: WARNING: py:obj reference target not found: emath.arcsin
docstring of numpy.arctanh:43: WARNING: py:obj reference target not found: emath.arctanh

in the resulting documentation build log file.

I was looking for where to edit the docstrings of these functions and ended up finding numpy/core/code_generators/ufunc_docstrings.py. Changing the docstrings in this file doesn't seem to change the docstrings in the resulting built numpy though. Is this the right file to edit?

@Mukulikaa
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Mukulikaa commented Feb 2, 2022 •
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Hi, @jon-deng. Did you rebuild NumPy before building the docs again? Just the docs rebuild will only reflect changes in *.rst files.

@gmarull gmarull mentioned this issue Feb 2, 2022
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jon-deng commented Feb 2, 2022

Hi @Mukulikaa. I did run pip install . on the numpy base directory before rebuilding the docs but I'm not sure if that will run the proper code to update docstrings? Could there be a problem in how I'm rebuilding numpy?

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Could there be a problem in how I'm rebuilding numpy?

No, I think you are doing it right. I'll try to recreate this locally and try a few things. Meanwhile, feel free to open a draft PR of your changes if you want :)

@jon-deng jon-deng mentioned this issue Feb 11, 2022
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I figured out the issue with the docs not appearing. When I called pip install . the old compiled C files were still there and for the ufuncs I think the build only generates documentation when the C files are compiled. I ran git clean -xdf to clear all the compiled files and rebuilding numpy showed the documentation changes.

@oscargus oscargus mentioned this issue Apr 4, 2022
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@bsipocz
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bsipocz commented May 22, 2022 •
edited

There are 188 of these remaining (full list in the details below), of which ~60 is due to `size` instead of ``size``, so that's a very low hanging fruit for someone with for a one-liner sed. There are a few other easy cases where args should be double backticked.
(Then of course fixing the last ~30% will be more tricky cases, but still, I feel there are a lot of easy ones in here)

@InessaPawson - maybe consider adding the sprint or good first issue back on this?

Edit: Since then I've learned that these linking issues should be resolved without doubling up on the backticks on parameters, and thus size will be a problematic case, and is not suitable as a first good issue.

writing output... [100%] user/whatisnumpy
/Users/bsipocz/munka/devel/numpy/doc/source/dev/internals.code-explanations.rst:272: WARNING: c:func reference target not found: PyArray_MapIterNew
/Users/bsipocz/munka/devel/numpy/doc/source/dev/internals.code-explanations.rst:284: WARNING: c:func reference target not found: PyArray_MapIterNew
/Users/bsipocz/munka/devel/numpy/doc/source/reference/arrays.classes.rst:516: WARNING: py:mod reference target not found: numpy.rec
/Users/bsipocz/munka/devel/numpy/doc/source/reference/arrays.dtypes.rst:164: WARNING: py:class reference target not found: character
/Users/bsipocz/munka/devel/numpy/doc/source/reference/arrays.dtypes.rst:164: WARNING: py:class reference target not found: string
/Users/bsipocz/munka/devel/numpy/doc/source/reference/arrays.dtypes.rst:188: WARNING: py:class reference target not found: buffer
/Users/bsipocz/munka/devel/numpy/doc/source/reference/arrays.dtypes.rst:304: WARNING: py:obj reference target not found: numpy.sctypeDict
/Users/bsipocz/munka/devel/numpy/doc/source/reference/arrays.interface.rst:175: WARNING: py:class reference target not found: buffer
/Users/bsipocz/munka/devel/numpy/doc/source/reference/arrays.interface.rst:249: WARNING: py:obj reference target not found: array_struct
/Users/bsipocz/munka/devel/numpy/doc/source/reference/arrays.ndarray.rst:24: WARNING: py:class reference target not found: buffer
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:701: WARNING: c:identifier reference target not found: FILE
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:851: WARNING: c:data reference target not found: PyGenericArr_Type
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:867: WARNING: c:data reference target not found: PyGenericArr_Type
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:873: WARNING: c:data reference target not found: PyGenericArr_Type
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:1087: WARNING: c:identifier reference target not found: PyArray_VectorUnaryFunc
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:1305: WARNING: c:identifier reference target not found: PyArray_VectorUnaryFunc
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:1711: WARNING: c:identifier reference target not found: FILE
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:2729: WARNING: c:identifier reference target not found: PyArrayMapIterObject
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:2737: WARNING: c:identifier reference target not found: PyArrayMapIterObject
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:3327: WARNING: c:identifier reference target not found: size_t
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:3334: WARNING: c:identifier reference target not found: size_t
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:3342: WARNING: c:identifier reference target not found: size_t
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:3344: WARNING: c:identifier reference target not found: size_t
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/array.rst:3355: WARNING: c:identifier reference target not found: size_t
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/data_memory.rst:102: WARNING: c:identifier reference target not found: size_t
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/iterator.rst:371: WARNING: c:identifier reference target not found: NpyIter_IterationNeedsAPI
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/iterator.rst:371: WARNING: c:identifier reference target not found: iter
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/types-and-structures.rst:592: WARNING: c:identifier reference target not found: FILE
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/types-and-structures.rst:968: WARNING: c:identifier reference target not found: PyUFunc_TypeResolutionFunc
/Users/bsipocz/munka/devel/numpy/doc/source/reference/c-api/types-and-structures.rst:977: WARNING: c:identifier reference target not found: PyUFunc_LegacyInnerLoopSelectionFunc
/Users/bsipocz/munka/devel/numpy/doc/source/reference/distutils.rst:12: WARNING: py:func reference target not found: core.setup
/Users/bsipocz/munka/devel/numpy/doc/source/reference/distutils.rst:12: WARNING: py:mod reference target not found: numpy.distutils.core
/Users/bsipocz/munka/devel/numpy/doc/source/reference/distutils.rst:180: WARNING: py:obj reference target not found: get_npy_pkg_dir
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.AxisError:16: WARNING: py:obj reference target not found: ndim
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.array:5: WARNING: py:mod reference target not found: numpy.core.defchararray
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.array:11: WARNING: py:obj reference target not found: unicode
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.array:48: WARNING: py:obj reference target not found: unicode
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.asarray:5: WARNING: py:obj reference target not found: unicode
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.chararray:5: WARNING: py:obj reference target not found: object_
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.chararray:5: WARNING: py:obj reference target not found: string_
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.chararray:5: WARNING: py:obj reference target not found: unicode_
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.chararray:53: WARNING: py:obj reference target not found: ndarray.strides
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.decode:33: WARNING: py:obj reference target not found: str.decode
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.isdecimal:5: WARNING: py:obj reference target not found: unicode.isdecimal
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.isdecimal:30: WARNING: py:obj reference target not found: unicode.isdecimal
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.isnumeric:5: WARNING: py:obj reference target not found: unicode.isnumeric
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.isnumeric:30: WARNING: py:obj reference target not found: unicode.isnumeric
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.mod:29: WARNING: py:obj reference target not found: str.mod
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.str_len:24: WARNING: py:obj reference target not found: builtins.len
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.chararray:11: WARNING: py:obj reference target not found: unicode
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.choose:4: WARNING: py:obj reference target not found: numpy.lib.index_tricks
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.array:5: WARNING: py:mod reference target not found: numpy.core.defchararray
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.array:11: WARNING: py:obj reference target not found: unicode
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.array:48: WARNING: py:obj reference target not found: unicode
/Users/bsipocz/munka/devel/numpy/numpy/core/defchararray.py:docstring of numpy.char.asarray:5: WARNING: py:obj reference target not found: unicode
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.correlate:41: WARNING: py:obj reference target not found: multiarray.correlate
/Users/bsipocz/munka/devel/numpy/numpy/distutils/ccompiler.py:docstring of numpy.distutils.ccompiler.CCompiler_customize_cmd:11: WARNING: py:obj reference target not found: CCompiler
/Users/bsipocz/munka/devel/numpy/numpy/distutils/ccompiler.py:docstring of numpy.distutils.ccompiler.CCompiler_cxx_compiler:13: WARNING: py:obj reference target not found: CCompiler
/Users/bsipocz/munka/devel/numpy/numpy/distutils/ccompiler.py:docstring of numpy.distutils.ccompiler.CCompiler_get_version:19: WARNING: py:obj reference target not found: distutils.version.LooseVersion
/Users/bsipocz/munka/devel/numpy/numpy/distutils/ccompiler.py:docstring of numpy.distutils.ccompiler.simple_version_match:24: WARNING: py:obj reference target not found: CCompiler
/Users/bsipocz/munka/devel/numpy/numpy/distutils/ccompiler_opt.py:docstring of numpy.distutils.ccompiler_opt.CCompilerOpt:61::1: WARNING: py:obj reference target not found: Config.conf_features
docstring of numpy.dtype.flags:4: WARNING: py:obj reference target not found: numpy.core.multiarray
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.einsum:77: WARNING: py:obj reference target not found: einops
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.einsum:79: WARNING: py:obj reference target not found: opt_einsum
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.expand_dims:42: WARNING: py:obj reference target not found: doc.indexing
docstring of numpy.invert:63: WARNING: py:obj reference target not found: bitwise_not
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.isscalar:24: WARNING: py:obj reference target not found: ndim
/Users/bsipocz/munka/devel/numpy/numpy/lib/arrayterator.py:docstring of numpy.lib.arrayterator.Arrayterator:34: WARNING: py:obj reference target not found: ndenumerate
/Users/bsipocz/munka/devel/numpy/numpy/lib/arrayterator.py:docstring of numpy.lib.arrayterator.Arrayterator:36: WARNING: py:obj reference target not found: flatiter
/Users/bsipocz/munka/devel/numpy/numpy/lib/arrayterator.py:docstring of numpy.lib.arrayterator.Arrayterator:38: WARNING: py:obj reference target not found: memmap
/Users/bsipocz/munka/devel/numpy/numpy/lib/arrayterator.py:docstring of numpy.lib.Arrayterator.flat:18: WARNING: py:obj reference target not found: Arrayterator
/Users/bsipocz/munka/devel/numpy/numpy/linalg/init.py:docstring of numpy.linalg.eig:61: WARNING: py:obj reference target not found: w
/Users/bsipocz/munka/devel/numpy/numpy/linalg/init.py:docstring of numpy.linalg.eig:61: WARNING: py:obj reference target not found: w
/Users/bsipocz/munka/devel/numpy/numpy/linalg/init.py:docstring of numpy.linalg.eigh:67: WARNING: py:obj reference target not found: w
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.ma.MaskedArray.array:: WARNING: py:class reference target not found: reference if type unchanged, copy otherwise.
/Users/bsipocz/munka/devel/numpy/numpy/ma/core.py:docstring of numpy.ma.core.MaskedArray.deepcopy:: WARNING: py:class reference target not found: Deep copy of array.
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.expand_dims:42: WARNING: py:obj reference target not found: doc.indexing
:1: WARNING: py:class reference target not found: numpy.ma.core.MaskedArray
docstring of numpy.ma.mr:4: WARNING: py:obj reference target not found: lib.index_tricks.RClass
docstring of numpy.ma.mr_:17: WARNING: py:obj reference target not found: lib.index_tricks.RClass
docstring of numpy.mgrid:4: WARNING: py:obj reference target not found: numpy.lib.index_tricks.nd_grid
docstring of numpy.mgrid:30: WARNING: py:obj reference target not found: lib.index_tricks.nd_grid
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.ndarray.array:: WARNING: py:class reference target not found: reference if type unchanged, copy otherwise.
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.ndarray.deepcopy:: WARNING: py:class reference target not found: Deep copy of array.
/Users/bsipocz/munka/devel/numpy/numpy/init.py:docstring of numpy.nditer:199: WARNING: py:obj reference target not found: exit
docstring of numpy.ogrid:4: WARNING: py:obj reference target not found: numpy.lib.index_tricks.nd_grid
docstring of numpy.ogrid:30: WARNING: py:obj reference target not found: np.lib.index_tricks.nd_grid
/Users/bsipocz/munka/devel/numpy/numpy/polynomial/_polybase.py:docstring of numpy.polynomial._polybase.ABCPolyBase.truncate:2: WARNING: py:obj reference target not found: size
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generating indices... genindex done
writing additional pages... search done
copying images... [100%] ../build/plot_directive/user/quickstart-2.png
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build finished with problems, 188 warnings.

<\details>

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InessaPawson commented Jun 16, 2022 •
edited

@bsipocz Good to know! Please ping me if you come across other issues that seem suitable for a sprint. (We don't use the good first issue label in NumPy.;) )

@bsipocz bsipocz added sprintable Issue fits the time-frame and setting of a sprint and removed sprintable Issue fits the time-frame and setting of a sprint labels Sep 16, 2022
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DOC: Fix bad reference in numpy.ma takanori-pskq/numpy