0.8.1: sphinx warnings reference target not found

[kloczek]

On building my packages I'm using sphinx-build command with -n switch which shows warmings about missing references. These are not critical issues.
There are few otgher warnings as well.
Here is the output with warnings:

+ /usr/bin/sphinx-build -n -T -b man docs build/sphinx/man
Running Sphinx v4.5.0
loading translations [en]... done
making output directory... done
myst v0.17.2: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence'], linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=2, heading_slug_func=None, footnote_transition=True, sub_delimiters=('{', '}'), words_per_minute=200)
[autosummary] generating autosummary for: contribute/index.md, contribute/manual.md, contribute/setup.md, contribute/topics.md, demo/api.rst, demo/example_pandas.rst, demo/index.rst, demo/kitchen-sink/api.rst, demo/kitchen-sink/index.rst, demo/kitchen-sink/lists-and-tables.rst, ..., demo/subpages/subsubpages/subsubpage8.rst, demo/subpages/subsubpages/subsubpage9.rst, demo/theme-elements.md, index.rst, user_guide/accessibility.rst, user_guide/configuring.rst, user_guide/customizing.rst, user_guide/index.rst, user_guide/install.rst, user_guide/sections.rst
[autosummary] generating autosummary for: /home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/generated/pandas.DataFrame.drop.rst, /home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/generated/pandas.DataFrame.groupby.rst, /home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/generated/pandas.Series.array.rst
building [mo]: targets for 0 po files that are out of date
building [man]: all manpages
updating environment: [new config] 48 added, 0 changed, 0 removed
executing theme-elements] demo/theme-elements
reading sources... [100%] user_guide/sections
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/api.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/index.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/lists-and-tables.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/paragraph-markup.rst.rst:229: WARNING: line number spec is out of range(1-10): '5-15'
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/paragraph-markup.rst:260: WARNING: Footnote [4] is not referenced.
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/paragraph-markup.rst:266: WARNING: Footnote [11] is not referenced.
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/paragraph-markup.rst:17: ERROR: Undefined substitution referenced: "problematic".
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/paragraph-markup.rst:260: ERROR: Unknown target name: "5".
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/paragraph-markup.rst:303: ERROR: Unknown target name: "body elements".
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/paragraph-markup.rst:315: ERROR: Unknown target name: "hyperlink reference without a target".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
writing... pydatasphinxtheme.1 { user_guide/index user_guide/install user_guide/configuring user_guide/sections user_guide/customizing user_guide/accessibility contribute/index contribute/setup contribute/topics contribute/manual demo/index demo/kitchen-sink/index demo/kitchen-sink/paragraph-markup demo/kitchen-sink/api demo/kitchen-sink/lists-and-tables demo/theme-elements demo/api demo/generated/pandas.DataFrame.drop demo/generated/pandas.DataFrame.groupby demo/generated/pandas.Series.array demo/example_pandas demo/no-sidebar demo/mult_headers demo/subpages/index demo/subpages/subpage1 demo/subpages/subpage2 demo/subpages/subsubpages/index demo/subpages/subsubpages/subsubpage1 demo/subpages/subsubpages/subsubpage2 demo/subpages/subsubpages/subsubpage3 demo/subpages/subsubpages/subsubpage4 demo/subpages/subsubpages/subsubpage5 demo/subpages/subsubpages/subsubpage6 demo/subpages/subsubpages/subsubpage7 demo/subpages/subsubpages/subsubpage8 demo/subpages/subsubpages/subsubpage9 demo/subpages/subsubpages/subsubpage10 demo/subpages/subsubpages/subsubpage11 demo/subpages/subsubpages/subsubpage12 demo/subpages/subsubpages/subsubpage13 demo/subpages/subsubpages/subsubpage14 demo/subpages/subsubpages/subsubpage15 demo/subpages/subsubpages/subsubpage16 demo/subpages/subsubpages/subsubpage17 demo/subpages/subsubpages/subsubpage18 demo/subpages/subsubpages/subsubpage19 demo/subpages/subsubpages/subsubpage20 } /home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/paragraph-markup.rst:26: WARNING: py:class reference target not found: test_py_module.test.Foo
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/paragraph-markup.rst:274: WARNING: citation not found: nonexistent
/usr/lib64/python3.8/asyncio/events.py:docstring of asyncio.events.AbstractEventLoop.create_datagram_endpoint:17: WARNING: py:data reference target not found: socket.SO_REUSEPORT
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.drop:: WARNING: py:class reference target not found: Axis
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.drop:: WARNING: py:class reference target not found: Level
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.drop:58: WARNING: py:obj reference target not found: DataFrame.loc
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.drop:60: WARNING: py:obj reference target not found: DataFrame.dropna
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.drop:62: WARNING: py:obj reference target not found: DataFrame.drop_duplicates
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.drop:64: WARNING: py:obj reference target not found: Series.drop
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.groupby:: WARNING: py:class reference target not found: Axis
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.groupby:: WARNING: py:class reference target not found: Level
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.groupby:: WARNING: py:class reference target not found: lib.NoDefault
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.groupby:: WARNING: py:class reference target not found: DataFrameGroupBy
/usr/lib64/python3.8/site-packages/pandas/core/frame.py:docstring of pandas.core.frame.DataFrame.groupby:75: WARNING: py:obj reference target not found: resample
/usr/lib64/python3.8/site-packages/pandas/core/series.py:docstring of pandas.Series.array:: WARNING: py:class reference target not found: pandas.core.arrays.base.ExtensionArray
/usr/lib64/python3.8/site-packages/pandas/core/series.py:docstring of pandas.Series.array:9: WARNING: py:class reference target not found: numpy.ndarray
/usr/lib64/python3.8/site-packages/pandas/core/series.py:docstring of pandas.Series.array:25: WARNING: py:obj reference target not found: Index.to_numpy
/usr/lib64/python3.8/site-packages/pandas/core/series.py:docstring of pandas.Series.array:27: WARNING: py:obj reference target not found: Series.to_numpy
/usr/lib64/python3.8/site-packages/pandas/core/series.py:docstring of pandas.Series.array:51: WARNING: py:class reference target not found: arrays.NumpyExtensionArray
/usr/lib64/python3.8/site-packages/pandas/core/series.py:docstring of pandas.Series.array:51: WARNING: py:meth reference target not found: Series.to_numpy
/usr/lib64/python3.8/site-packages/numpy/linalg/__init__.py:docstring of numpy.linalg.eig:39: WARNING: py:obj reference target not found: eigvals
/usr/lib64/python3.8/site-packages/numpy/linalg/__init__.py:docstring of numpy.linalg.eig:41: WARNING: py:obj reference target not found: eigh
/usr/lib64/python3.8/site-packages/numpy/linalg/__init__.py:docstring of numpy.linalg.eig:43: WARNING: py:obj reference target not found: eigvalsh
/usr/lib64/python3.8/site-packages/numpy/linalg/__init__.py:docstring of numpy.linalg.eig:45: WARNING: py:obj reference target not found: scipy.linalg.eig
/usr/lib64/python3.8/site-packages/numpy/linalg/__init__.py:docstring of numpy.linalg.eig:47: WARNING: py:obj reference target not found: scipy.linalg.schur
/usr/lib64/python3.8/site-packages/numpy/linalg/__init__.py:docstring of numpy.linalg.norm:50: WARNING: py:obj reference target not found: scipy.linalg.norm
/usr/lib64/python3.8/site-packages/numpy/linalg/__init__.py:docstring of numpy.linalg.tensorinv:37: WARNING: py:obj reference target not found: numpy.tensordot
/usr/lib64/python3.8/site-packages/numpy/linalg/__init__.py:docstring of numpy.linalg.tensorinv:37: WARNING: py:obj reference target not found: tensorsolve
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/api.rst:51: WARNING: cpp:identifier reference target not found: Sphinx
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/api.rst:78: WARNING: cpp:identifier reference target not found: MySpecificEnum
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/api.rst:103: WARNING: js:class reference target not found: ModTopLevel
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:785: WARNING: py:meth reference target not found: pandas.DataFrame.query
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:788: WARNING: py:class reference target not found: pandas.DataFrame
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:788: WARNING: py:meth reference target not found: pandas.DataFrame.query
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:848: WARNING: py:class reference target not found: pandas.MultiIndex
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:848: WARNING: py:meth reference target not found: pandas.DataFrame.query
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:851: WARNING: py:class reference target not found: pandas.MultiIndex
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:881: WARNING: py:meth reference target not found: pandas.DataFrame.query
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:884: WARNING: py:meth reference target not found: pandas.DataFrame.query
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:884: WARNING: py:class reference target not found: pandas.DataFrame
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:898: WARNING: py:meth reference target not found: pandas.DataFrame.query
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/example_pandas.rst:932: WARNING: py:meth reference target not found: pandas.DataFrame.query
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/lists-and-tables.rst:: WARNING: "table cell spanning" not supported
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/lists-and-tables.rst:: WARNING: "table row spanning" not supported
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/lists-and-tables.rst:: WARNING: "table row spanning" not supported
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/lists-and-tables.rst:: WARNING: "table cell spanning" not supported
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/lists-and-tables.rst:: WARNING: "table cell spanning" not supported
/home/tkloczko/rpmbuild/BUILD/pydata-sphinx-theme-0.8.1/docs/demo/kitchen-sink/lists-and-tables.rst:: WARNING: "table cell spanning" not supported
done
build succeeded, 58 warnings.

[kloczek]

One more thiong. Top be able use sphinx-buil it is necessary to apply below patch which applies what exactly is mentioned in comment above added lines

+++ b/docs/conf.py      2022-04-29 10:25:21.499346864 +0000
@@ -11,10 +11,8 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
+import sys
+sys.path.insert(0, os.path.abspath('../src'))

 # -- Project information -----------------------------------------------------

[12rambau]

I think the warning behavior is expected as pydata-sphinx-theme only imports part of pandas for the demo.

on the sphinx-build command, we are using it to build the documentation both in our tests and the RTD website so I don't know what's wrong from your side that requires you to change the conf.py file. Could you try again using the 0.9.0 version ?

[kloczek]

You can peak on fixes that kind of issues in other projects
latchset/jwcrypto#289
click-contrib/sphinx-click@abc31069
latchset/jwcrypto#289
RDFLib/rdflib-sqlalchemy#95
sissaschool/elementpath@bf869d9e
jaraco/cssutils#21

[12rambau]

same comment as for #902

agree with @choldgraf that we (maintainers) are already over-subscribed. If this is something you really want @kloczek you'll need to do the debugging yourself and open a PR; if it doesn't add too much complexity I'd be willing to merge it. But it sounds like you don't even use the theme (?) and you're doing this as a sort of... public service? quixotic pet project? not sure what to call it, so maybe that's a non-starter for you. I'll close on that assumption, but let us know if I'm wrong about that and we can re-open in anticipation of your PR.

[drammock]

Just as an FYI @kloczek : the warnings and errors on the "kitchen sink" page are expected because part of the point of that page is to demo all formatting, including things like broken references.