Update sphinx to 4.4

[antonio-rojas]

Throws warnings (which abort the doc build) when a role can be used but it's not.

CC: @kiwifb @tobihan @collares @kwankyu

Component: packages: standard

Author: Antonio Rojas, François Bissey

Branch/Commit: 17fa6d4

Reviewer: Kwankyu Lee

Issue created by migration from https://trac.sagemath.org/ticket/33272

[antonio-rojas]

Branch: u/arojas/update_sphinx_to_4_4

[antonio-rojas]

Commit: e14fe07

[antonio-rojas]

Description changed:

--- 
+++ 
@@ -1 +1 @@
-
+Throws warnings (which abort the doc build) when a role can be used but it's not.

[antonio-rojas]

Author: Antonio Rojas

[antonio-rojas]

New commits:

97d7958	Use roles when possible to fix warnings
e14fe07	Update Sphinx to 4.4.0

[mkoeppe]

comment:3

The changes in build/ and pkgs/ are not good because they are intended to be readable also by themselves, without running them through our Sphinx docbuild. For example, the pkgs/*/README.rst appear on PyPI.

[mkoeppe]

comment:4

Perhaps these substitutions can be made in the src/doc/bootstrap script

[kiwifb]

comment:6

Upgrade to sphinx 4.3.1 (#32968) is currently being merged by Volker and will be in the next beta. So this ticket will need rebasing on top of it. And I am surprised you don't seem to need https://github.com/sagemath/sagetrac-mirror/commit/fc84f82f52b6f05f512cb359ec7c100f93cf8841 - but looking more closely, all your work with changing external references around may be helping with that. We may need careful navigating around that line.

[antonio-rojas]

comment:7

Replying to @kiwifb:

Upgrade to sphinx 4.3.1 (#32968) is currently being merged by Volker and will be in the next beta.

Yes, I'm aware. This was tested and needs to be merged on top of that. I will rebase after the next beta.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from e14fe07 to 489ad27

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

489ad27

Merge remote-tracking branch 'origin' into t/33272/update_sphinx_to_4_4

[collares]

comment:9

Note that these warnings will probably be disabled by default in Sphinx 4.4.1: https://github.com/sphinx-doc/sphinx/pull/10126

[kiwifb]

comment:10

Trying this in sage-on-gentoo since sphinx-4.4.0 is now stable. I get

[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/_bootstrap.rst:111: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
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[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/cunningham_tables.rst:30: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
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[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/database_cremona_ellcurve.rst:75: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
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[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/database_knotinfo.rst:44: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
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[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/database_odlyzko_zeta.rst:39: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
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[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/sphinxcontrib_websupport.rst:58: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/sqlalchemy.rst:66: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/surf.rst:70: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/surface_dynamics.rst:42: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/symengine.rst:79: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/symengine_py.rst:53: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/sympy.rst:84: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/tdlib.rst:63: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/terminado.rst:57: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/testpath.rst:53: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/texttable.rst:65: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/thebe.rst:61: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/threejs.rst:60: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/tides.rst:57: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/tomli.rst:49: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/topcom.rst:71: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/tornado.rst:75: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/traitlets.rst:70: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/typing_extensions.rst:51: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/tzlocal.rst:59: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/urllib3.rst:51: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/valgrind.rst:102: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/vcversioner.rst:70: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/wcwidth.rst:70: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/webencodings.rst:75: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/wheel.rst:71: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/widgetsnbextension.rst:87: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/zipp.rst:68: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/29023' could be replaced by an extlink (try using ':trac:`ticket/29023`' instead)
[spkg     ] The inventory files are in ../../../build_doc/inventory/en/reference/spkg.
Error building the documentation.
Traceback (most recent call last):
  File "/usr/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/usr/lib/python3.10/site-packages/sage_docbuild/__main__.py", line 2, in <module>
    main()
  File "/usr/lib/python3.10/site-packages/sage_docbuild/__init__.py", line 1741, in main
    builder()
  File "/usr/lib/python3.10/site-packages/sage_docbuild/__init__.py", line 781, in _wrapper
    getattr(DocBuilder, build_type)(self, *args, **kwds)
  File "/usr/lib/python3.10/site-packages/sage_docbuild/__init__.py", line 136, in f
    runsphinx()
  File "/usr/lib/python3.10/site-packages/sage_docbuild/sphinxbuild.py", line 326, in runsphinx
    sys.stderr.raise_errors()
  File "/usr/lib/python3.10/site-packages/sage_docbuild/sphinxbuild.py", line 262, in raise_errors
    raise OSError(self._error)
OSError: /dev/shm/portage/sci-mathematics/sage-doc-9999/work/sage-doc-9999/src/doc/en/reference/spkg/_bootstrap.rst:111: WARNING: hardcoded link 'https://github.com/sagemath/sage-prod/issues/27330' could be replaced by an extlink (try using ':trac:`ticket/27330`' instead)

[kiwifb]

Changed branch from u/arojas/update_sphinx_to_4_4 to u/fbissey/sphinx-4.4

[kiwifb]

Changed commit from 489ad27 to c839fe7

[kiwifb]

comment:11

Still building, have trouble with stuff coming from #33309 at the same time on the branch Volker is merging tickets. But that got rid of all those so called warnings that break the build.

---

New commits:

42c636e	Merge branch 'develop' into sphinx-4.4
c839fe7	convert all links to trac to extlink during bootstrap

[kiwifb]

comment:12

Build failed on pdf with some undefined references. Will try html only to see if that works.

  Citation `algebraic_combinatorics/tsetlin_library:aks2013' on page 32 undefined on input line 1003
  Citation `algebraic_combinatorics/tsetlin_library:bidigare1997' on page 32 undefined on input line 999
  Citation `algebraic_combinatorics/tsetlin_library:brown2000' on page 32 undefined on input line 1000
  Citation `algebraic_combinatorics:stanley2013' on page 25 undefined on input line 541
  Citation `algebraic_combinatorics:stanley2013' on page 27 undefined on input line 651
  Citation `algebraic_combinatorics:stanley2013' on page 32 undefined on input line 1011
  Citation `lie/bibliography:bourbaki46' on page 134 undefined on input line 9789
  Citation `lie/bibliography:bourbaki46' on page 134 undefined on input line 9791
  Citation `lie/bibliography:bourbaki46' on page 134 undefined on input line 9802
  Citation `lie/bibliography:bumpnakasuji2010' on page 171 undefined on input line 12819
  Citation `lie/bibliography:carrell1994' on page 171 undefined on input line 12807
  Citation `lie/bibliography:deodhar1977' on page 171 undefined on input line 12811
  Citation `lie/bibliography:dyer1993' on page 171 undefined on input line 12815
  Citation `lie/bibliography:dynkin1952' on page 152 undefined on input line 11245
  Citation `lie/bibliography:fauseretal2006' on page 152 undefined on input line 11223
  Citation `lie/bibliography:fourieretal2009' on page 198 undefined on input line 14967
  Citation `lie/bibliography:fourieretal2009' on page 198 undefined on input line 14974
  Citation `lie/bibliography:fourieretal2010' on page 210 undefined on input line 15516
  Citation `lie/bibliography:fulton1997' on page 174 undefined on input line 13054
  Citation `lie/bibliography:hatayamaetal2001' on page 198 undefined on input line 14972
  Citation `lie/bibliography:hongkang2002' on page 142 undefined on input line 10461
  Citation `lie/bibliography:hongkang2002' on page 176 undefined on input line 13199
  Citation `lie/bibliography:hongkang2002' on page 179 undefined on input line 13440
  Citation `lie/bibliography:hongkang2002' on page 210 undefined on input line 15515
  Citation `lie/bibliography:hongkang2002' on page 210 undefined on input line 15553
  Citation `lie/bibliography:honglee2008' on page 218 undefined on input line 16017
  Citation `lie/bibliography:howeetal2005' on page 152 undefined on input line 11231
  Citation `lie/bibliography:iwahori1964' on page 225 undefined on input line 16349
  Citation `lie/bibliography:jaynemisra2014' on page 197 undefined on input line 14926
  Citation `lie/bibliography:jimbo1986' on page 175 undefined on input line 13180
  Citation `lie/bibliography:jonesetal2010' on page 207 undefined on input line 15405
  Citation `lie/bibliography:joseph1995' on page 216 undefined on input line 15893
  Citation `lie/bibliography:joseph1995' on page 216 undefined on input line 15894
  Citation `lie/bibliography:kac' on page 134 undefined on input line 9791
  Citation `lie/bibliography:kac' on page 142 undefined on input line 10422
  Citation `lie/bibliography:kac' on page 142 undefined on input line 10425
  Citation `lie/bibliography:kac' on page 142 undefined on input line 10461
  Citation `lie/bibliography:kac' on page 187 undefined on input line 14081
  Citation `lie/bibliography:kac' on page 188 undefined on input line 14098
  Citation `lie/bibliography:kac' on page 188 undefined on input line 14162
  Citation `lie/bibliography:kac' on page 190 undefined on input line 14279
  Citation `lie/bibliography:kac' on page 191 undefined on input line 14413
  Citation `lie/bibliography:kac' on page 191 undefined on input line 14422
  Citation `lie/bibliography:kac' on page 191 undefined on input line 14429
  Citation `lie/bibliography:kac' on page 191 undefined on input line 14450
  Citation `lie/bibliography:kac' on page 192 undefined on input line 14470
  Citation `lie/bibliography:kac' on page 195 undefined on input line 14698
  Citation `lie/bibliography:kac' on page 195 undefined on input line 14702
  Citation `lie/bibliography:kac' on page 195 undefined on input line 14726
  Citation `lie/bibliography:kac' on page 195 undefined on input line 14754
  Citation `lie/bibliography:kacpeterson' on page 195 undefined on input line 14724
  Citation `lie/bibliography:kacpeterson' on page 195 undefined on input line 14755
  Citation `lie/bibliography:kacpeterson' on page 197 undefined on input line 14898
  Citation `lie/bibliography:kashiwara1993' on page 214 undefined on input line 15772
  Citation `lie/bibliography:kashiwara1993' on page 215 undefined on input line 15839
  Citation `lie/bibliography:kashiwara1993' on page 217 undefined on input line 15965
  Citation `lie/bibliography:kashiwara1995' on page 176 undefined on input line 13191
  Citation `lie/bibliography:kashiwara1995' on page 214 undefined on input line 15773
  Citation `lie/bibliography:kashiwara1995' on page 217 undefined on input line 15965
  Citation `lie/bibliography:kashiwaranakashima1994' on page 176 undefined on input line 13195
  Citation `lie/bibliography:kashiwaranakashima1994' on page 179 undefined on input line 13439
  Citation `lie/bibliography:kimleeoh2017' on page 197 undefined on input line 14926
  Citation `lie/bibliography:kimshin2010' on page 221 undefined on input line 16117
  Citation `lie/bibliography:king1975' on page 152 undefined on input line 11227
  Citation `lie/bibliography:kkmmnn1992' on page 210 undefined on input line 15552
  Citation `lie/bibliography:kks2007' on page 213 undefined on input line 15719
  Citation `lie/bibliography:kks2007' on page 223 undefined on input line 16248
  Citation `lie/bibliography:kmps' on page 187 undefined on input line 14082
  Citation `lie/bibliography:kmps' on page 192 undefined on input line 14471
  Citation `lie/bibliography:kmps' on page 194 undefined on input line 14648
  Citation `lie/bibliography:kmps' on page 194 undefined on input line 14666
  Citation `lie/bibliography:kmps' on page 194 undefined on input line 14670
  Citation `lie/bibliography:kmps' on page 197 undefined on input line 14898
  Citation `lie/bibliography:knuth1970' on page 174 undefined on input line 13050
  Citation `lie/bibliography:knuth1998' on page 174 undefined on input line 13046
  Citation `lie/bibliography:l1995' on page 212 undefined on input line 15657
  Citation `lie/bibliography:lnsss14i' on page 209 undefined on input line 15479
  Citation `lie/bibliography:lnsss14ii' on page 209 undefined on input line 15479
  Citation `lie/bibliography:macdonald2003' on page 190 undefined on input line 14280
  Citation `lie/bibliography:mckaypatera1981' on page 152 undefined on input line 11235
  Citation `lie/bibliography:mckaypatera1981' on page 165 undefined on input line 12377
  Citation `lie/bibliography:okadoschilling2008' on page 198 undefined on input line 14973
  Citation `lie/bibliography:rubenthaler2008' on page 163 undefined on input line 12260
  Citation `lie/bibliography:salisburyscrimshaw2015' on page 225 undefined on input line 16312
  Citation `lie/bibliography:schilling2006' on page 225 undefined on input line 16311
  Citation `lie/bibliography:schillingtingley2011' on page 211 undefined on input line 15582
  Citation `lie/bibliography:seitz1991' on page 163 undefined on input line 12269
  Citation `lie/bibliography:seitz1991' on page 164 undefined on input line 12290
  Citation `lie/bibliography:seitz1991' on page 164 undefined on input line 12294
  Citation `lie/bibliography:stanley1999' on page 174 undefined on input line 13058
  Citation `lie/bibliography:testerman1989' on page 163 undefined on input line 12232
  Citation `lie/bibliography:testerman1992' on page 164 undefined on input line 12306
  Citation `sandpile:bn' on page 35 undefined on input line 1187
  Citation `sandpile:bn' on page 41 undefined on input line 1637
  Citation `sandpile:btw' on page 40 undefined on input line 1583
  Citation `sandpile:crs' on page 43 undefined on input line 1786
  Citation `sandpile:h' on page 35 undefined on input line 1185
  Citation `sandpile:levine2014' on page 72 undefined on input line 4280
  Citation `sandpile:levine2014' on page 83 undefined on input line 5232
  Citation `sandpile:ppw2013' on page 35 undefined on input line 1187

Overfull \vbox (2.72194pt too high) detected at line 17996
[223] [74] [2985] [75] [2986] [224] [76]
Underfull \hbox (badness 10000) in paragraph at lines 286330--286332
[]\T1/qtm/m/n/10 Bases: [][]\T1/txtt/m/n/10 sage.structure.unique_representatio
n.UniqueRepresentation[][]\T1/qtm/m/n/10 , [][]\T1/txtt/m/n/10 sage.structure.
 [77[2987]] [225 [78]]
Chapter 14.
 [2988] [226[79]]Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 102 citation(s)
Latexmk: Errors, so I did not complete making targets
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'thematic_tutorials.log' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
make[2]: *** [Makefile:29: thematic_tutorials.pdf] Error 12
make[2]: Leaving directory '/dev/shm/portage/sci-mathematics/sage-doc-9999/work/build_doc/latex/en/thematic_tutorials'
Error building the documentation.
Traceback (most recent call last):
  File "/usr/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/usr/lib/python3.10/site-packages/sage_docbuild/__main__.py", line 2, in <module>
    main()
  File "/usr/lib/python3.10/site-packages/sage_docbuild/__init__.py", line 1745, in main
    builder()
  File "/usr/lib/python3.10/site-packages/sage_docbuild/__init__.py", line 270, in pdf
    raise RuntimeError(error_message % (command, tex_dir))
RuntimeError: failed to run $MAKE all-pdf in /dev/shm/portage/sci-mathematics/sage-doc-9999/work/build_doc/latex/en/thematic_tutorials

    Note: incremental documentation builds sometimes cause spurious
    error messages. To be certain that these are real errors, run
    "make doc-clean doc-uninstall" first and try again.

[kiwifb]

comment:13

Building html only does work.

[kiwifb]

comment:14

Citations are not relevant in the end I think. From thematic_tutorials.log

<vector_calc_change-1.pdf, id=1696, 462.52798pt x 346.89601pt>
File: vector_calc_change-1.pdf Graphic file (type pdf)
<use vector_calc_change-1.pdf>
Package pdftex.def Info: vector_calc_change-1.pdf  used on input line 17866.
(pdftex.def)             Requested size: 462.52684pt x 346.89516pt.
<vector_calc_change-2.pdf, id=1698, 462.52798pt x 346.89601pt>
File: vector_calc_change-2.pdf Graphic file (type pdf)
<use vector_calc_change-2.pdf>
Package pdftex.def Info: vector_calc_change-2.pdf  used on input line 17904.
(pdftex.def)             Requested size: 462.52684pt x 346.89516pt.
[246] [247 <./vector_calc_change-1.pdf>] [248 <./vector_calc_change-2.pdf>]
<vector_calc_change-3.pdf, id=1731, 462.52798pt x 346.89601pt>
File: vector_calc_change-3.pdf Graphic file (type pdf)
<use vector_calc_change-3.pdf>
Package pdftex.def Info: vector_calc_change-3.pdf  used on input line 17920.
(pdftex.def)             Requested size: 462.52684pt x 346.89516pt.

[249 <./vector_calc_change-3.pdf>] [250] [251] [252] [253] [254] [255]
! You can't use `macro parameter character #' in math mode.
l.18491 ...n the future, see the discussion at \(#
                                                  24456
? 
! Emergency stop.
l.18491 ...n the future, see the discussion at \(#
                                                  24456
End of file on the terminal!

Here is how much of TeX's memory you used:
 14921 strings out of 479658
 213909 string characters out of 5878930
 707354 words of memory out of 5000000
 31095 multiletter control sequences out of 15000+600000
 468261 words of font info for 90 fonts, out of 8000000 for 9000
 817 hyphenation exceptions out of 8191
 83i,29n,88p,888b,587s stack positions out of 5000i,500n,10000p,200000b,80000s
!  ==> Fatal error occurred, no output PDF file produced!

[kiwifb]

comment:15

OK, it looks like stuff like #ticket_number has to go. In fact from the output I saw earlier today, we need to move from :trac:`ticket/29023` to :trac:`29023`.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from c839fe7 to ab2365c

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

ab2365c

remove superfluous "ticket/"

[kiwifb]

comment:17

I am not saying it should be the definitive form, especially in the stuff I changed in the thematic_tutorials, but it now builds both the html and the pdf without a hitch.

Pitty I am doing all that remotely, I will have to wait tomorrow to see what it looks like.

@kwankyu copying you because you care about the doc so you can give us your opinion about how it looks like after the upgrade and whether we need to improve our output.

[kiwifb]

Changed author from Antonio Rojas to Antonio Rojas, François Bissey

[kwankyu]

comment:18

I get this error when make:

sed: -I or -i may not be used with stdin

My system is macOS Monterey.

[mkoeppe]

comment:19

Yes, sed -i is not portable; so sed should instead be used in a pipe

[mkoeppe]

comment:20

Also comment:3 is not fully addressed yet - the changes to pkgs/*/README.rst are not good

[kiwifb]

comment:21

Yes, I should have known sed -i would cause trouble. On the other hand I should be able to revert those build/*/*.rst and pkgs/*/*.rst changes by using the same formula. Although it gets a bit annoying when it involves other stuff than trac.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from ab2365c to d527946

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

cedcfff	We don't need to touch any README.rst as they are not used to build the documentation
e8e80f3	Revert changes to `SPKG.rst`s, those changes can be applied when bootstraping the documentation
d527946	be more portable, do not use `sed -i`, pipe sed into the writing process.

[kiwifb]

comment:23

OK, this builds here. I piped sed as suggested so it should be more portable and I addressed comment:3 by reverting the changes in question completely. The changes to README.rst were not useful as they are not used when building the documentation. The changes to SPKG.rst files can be applied on the fly when bootstrapping src/doc/en/reference/spkg/ like I do with all other such files.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

a29f778

reverting changes to sage-spkg-info

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from d527946 to a29f778

[kiwifb]

comment:25

I don't think the changes to sage-spkg-info made sense either. Like for README.rst they are meant to be readable, they are normally issued as part of the configure process. Any such statement should be converted during bootstrap as well.

[kiwifb]

comment:26

Much more work to do from the output I get. Constructs like

`some text <https://someadress>`_

work fine but

`this text <:trac:`12345`>`_

doesn't at all. It displays thistext <:trac:>`_ in italics. The lack of space between this and text is not a mistake, it is really not present in the output. The final underscore may not be in italics but that's hard to establish and it shouldn't be visible in the first place.

:trac: is just an example, :wikipedia: behaves the same way and I expect all handles will be the same. Whatever the correct thing to do is, we will have to comb the whole thing to update the syntax.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

1d8a60d

removing some bracket that produce no interesting output and do not improve readibility.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from a29f778 to 1d8a60d

[kiwifb]

comment:28

I am not sure who tried to mix extlinks and rst caption links first. But it could hardly work, extlinks are already providing a, pre-formatted, captioned link. If you want a different caption, you shouldn't use extlinks - which of course currently gives us an error.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

5251eb6

Update the formating of extlinks in accordance with https://sphinx-doc.org/en/master/usage/extensions/extlinks.html - this seem to be a sphinx 4.0 change.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from 1d8a60d to 5251eb6

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from 5251eb6 to 7230e35

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

7230e35

fix broken link constructs - prototypes

[kiwifb]

comment:31

Following sphinx documentation, structure like

`this text <:trac:`12345`>`_

need to be replaced by

:trac:`this text <12345>`

The html output is good, and I put some samples on the branch. I am checking that pdf builds with this as well before going any further.

[kiwifb]

comment:32

pdf builds and looks good :)

[strogdon]

comment:33

Unable to download sphinx here. Things like

http://files.sagemath.org/spkg/upstream/sphinx/Sphinx-4.4.0.tar.gz
[xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: '//files.sagemath.org/spkg/upstream/sphinx/Sphinx-4.4.0.tar.gz'

for all available mirrors. Will the Gentoo available tarball work?

[strogdon]

comment:34

The Gentoo available one works.

[kiwifb]

comment:35

Yes, you beat me to it. There is another way to download the sources from within sage but I always forget it.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from 7230e35 to 7d373f0

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

7d373f0

fix a forgotten "ticket/" entry

[kiwifb]

comment:37

I am fixing the formatting of all the files in the current branch first. Then I'll see if there are any other that lurk around in the rest of sage.