sage.coding: Modularization fixes, doctest cosmetics, add `# optional` #35729

mkoeppe · 2023-06-05T06:19:58Z

📚 Description

Modularization fixes for imports (using lazy_import, moving imports from module level to method level).

Adding a header line # sage.doctest: optional - sage.modules sage.rings.finite_rings to most files.

Adding some more # optional to doctest lines.

Some markup fixes for the documentation (such as fixing the accidental boxes around nest enumerations: https://doc.sagemath.org/html/en/reference/coding/sage/coding/guruswami_sudan/gs_decoder.html#sage.coding.guruswami_sudan.gs_decoder.GRSGuruswamiSudanDecoder)

Some reformatting of doctests so they can be read in HTML format without horizontal scrolling.
For example, fixing the documentation of AbstractLinearCode.automorphism_group_gens (new: https://deploy-preview-35729--sagemath-tobias.netlify.app/reference/coding/sage/coding/linear_code.html#sage.coding.linear_code.AbstractLinearCode.automorphism_group_gens)

📝 Checklist

The title is concise, informative, and self-explanatory.
The description explains in detail what this PR is about.
I have linked a relevant issue or discussion.
I have created tests covering the changes.
I have updated the documentation accordingly.

⌛ Dependencies

dimpase · 2023-06-06T16:24:23Z

test fails:

 DeprecationWarning: invalid escape sequence \G
**********************************************************************
1 item had failures:
   1 of  90 in doc.en.thematic_tutorials.coding_theory

mkoeppe · 2023-06-06T23:40:02Z

the timeout in fusion_ring is unrelated

dimpase · 2023-06-07T15:57:02Z

pdf docs doesn't build, with an error I never saw:

2023-06-07T14:21:54.4330040Z [sagemath_doc_pdf-none] Rule 'pdflatex': File changes, etc:
2023-06-07T14:21:54.4330532Z [sagemath_doc_pdf-none]    Changed files, or newly in use since previous run(s):
2023-06-07T14:21:54.4331087Z [sagemath_doc_pdf-none]       '/root/.texlive2019/texmf-var/web2c/pdftex/pdflatex.fmt'
2023-06-07T14:21:54.4331675Z [sagemath_doc_pdf-none] Latexmk: Maximum runs of pdflatex reached without getting stable files
2023-06-07T14:21:54.4332205Z [sagemath_doc_pdf-none] Latexmk: Summary of warnings from last run of *latex:
2023-06-07T14:21:54.4332748Z [sagemath_doc_pdf-none]   =====Latex reported missing or unavailable character(s).
2023-06-07T14:21:54.4333221Z [sagemath_doc_pdf-none] =====See log file for details.
2023-06-07T14:21:54.4333675Z [sagemath_doc_pdf-none]   Latex failed to resolve 1015 citation(s)
2023-06-07T14:21:54.4334086Z [sagemath_doc_pdf-none] ----------------------
2023-06-07T14:21:54.4334541Z [sagemath_doc_pdf-none] This message may duplicate earlier message.
2023-06-07T14:21:54.4335054Z [sagemath_doc_pdf-none] Latexmk: Failure in processing file 'combinat.tex':
2023-06-07T14:21:54.4335524Z [sagemath_doc_pdf-none]    'pdflatex' needed too many passes
2023-06-07T14:21:54.4335944Z [sagemath_doc_pdf-none] ----------------------
2023-06-07T14:21:54.4336433Z [sagemath_doc_pdf-none] Latexmk: Use the -f option to force complete processing,
2023-06-07T14:21:54.4336998Z [sagemath_doc_pdf-none]  unless error was exceeding maximum runs, or warnings treated as errors.
2023-06-07T14:21:54.4337501Z [sagemath_doc_pdf-none] Latexmk: Examining 'combinat.log'
2023-06-07T14:21:54.4338046Z [sagemath_doc_pdf-none] === TeX engine is 'pdfTeX'
2023-06-07T14:21:54.4338497Z [sagemath_doc_pdf-none] Latexmk: applying rule 'pdflatex'...
2023-06-07T14:21:54.4338978Z [sagemath_doc_pdf-none] Latexmk: All targets (combinat.pdf) are up-to-date
2023-06-07T14:21:54.4339491Z [sagemath_doc_pdf-none] make[5]: *** [Makefile:29: combinat.pdf] Error 12
2023-06-07T14:21:54.4339953Z [sagemath_doc_pdf-none] Error building the documentation.
2023-06-07T14:21:54.4340386Z [sagemath_doc_pdf-none] Traceback (most recent call last):
2023-06-07T14:21:54.4340883Z [sagemath_doc_pdf-none]   File "<frozen runpy>", line 198, in _run_module_as_main
2023-06-07T14:21:54.4341375Z [sagemath_doc_pdf-none]   File "<frozen runpy>", line 88, in _run_code
2023-06-07T14:21:54.4342077Z [sagemath_doc_pdf-none]   File "/__w/sage/sage/pkgs/sage-docbuild/sage_docbuild/__main__.py", line 498, in <module>
2023-06-07T14:21:54.4342542Z [sagemath_doc_pdf-none]     sys.exit(main())
2023-06-07T14:21:54.4343043Z [sagemath_doc_pdf-none]              ^^^^^^
2023-06-07T14:21:54.4343609Z [sagemath_doc_pdf-none]   File "/__w/sage/sage/pkgs/sage-docbuild/sage_docbuild/__main__.py", line 495, in main
2023-06-07T14:21:54.4344052Z [sagemath_doc_pdf-none]     builder()
2023-06-07T14:21:54.4344590Z [sagemath_doc_pdf-none]   File "/__w/sage/sage/pkgs/sage-docbuild/sage_docbuild/builders.py", line 299, in pdf
2023-06-07T14:21:54.4345165Z [sagemath_doc_pdf-none]     raise RuntimeError(error_message % (command, tex_dir))
2023-06-07T14:21:54.4345788Z [sagemath_doc_pdf-none] RuntimeError: failed to run $MAKE all-pdf in /sage/local/share/doc/sage/latex/en/reference/combinat
2023-06-07T14:21:54.4346241Z [sagemath_doc_pdf-none] 
2023-06-07T14:21:54.4346725Z [sagemath_doc_pdf-none]     Note: incremental documentation builds sometimes cause spurious
2023-06-07T14:21:54.4347301Z [sagemath_doc_pdf-none]     error messages. To be certain that these are real errors, run
2023-06-07T14:21:54.4347908Z [sagemath_doc_pdf-none]     "make doc-clean doc-uninstall" first and try again.

mkoeppe · 2023-06-07T16:50:47Z

Is that a local pdf build or are you reading this from the "CI PDF", which is known to be broken?

dimpase · 2023-06-07T18:14:48Z

CI pdf. Is it broken?

mkoeppe · 2023-06-07T18:31:37Z

Yes, it's broken, related to running tex as root with a weird home directory configuration

dimpase · 2023-06-07T19:45:39Z

hmm, is there an issue for this?

mkoeppe · 2023-06-07T20:00:17Z

Not yet; I haven't paged this out from my brain to a GH Issue. Tobias disabled the workflow in sagemath/sage, so there is no urgency

dcoudert · 2023-06-10T10:48:35Z

src/sage/coding/abstract_code.py

@@ -196,7 +197,7 @@ class AbstractCode(Parent):
      ``MyDecoderClass``.


-    As AbstractCode is not designed to be implemented, it does not have any
+    As the class :class:`AbstractCode` is not designed to be instantiated, it does not have any


80 columns mode

Fixed many of these in a67136a

src/sage/coding/binary_code.pyx

dcoudert · 2023-06-10T11:00:04Z

src/sage/coding/linear_code.py

            7920
-            sage: G = C.permutation_automorphism_group()  # long time (6s on sage.math, 2011)
-            sage: G.is_isomorphic(M11)                    # long time
+            sage: G = C.permutation_automorphism_group()  # long time (6s on sage.math, 2011)   # optional - sage.groups


May be we should update these long time statements. It should now be much less than the 6s of 2011 ;)

I agree; comments like this make our codebase look dated.

Probably best done in a separate PR, for all such annotations at the same time.

src/sage/coding/linear_code_no_metric.py

github-actions · 2023-06-10T20:34:34Z

Documentation preview for this PR (built with commit 5aac3bf) is ready! 🎉

dcoudert

LGTM.

mkoeppe · 2023-06-11T15:45:59Z

Thanks a lot!

sage.coding: Doctest cosmetics, add # optional

6d3bc3e

mkoeppe added c: coding theory t: refactoring labels Jun 5, 2023

mkoeppe self-assigned this Jun 5, 2023

Matthias Koeppe added 3 commits June 4, 2023 23:40

src/sage/coding/guruswami_sudan/gs_decoder.py: Fix doc markup

abe201e

Fix up super in doctests

c718341

src/sage/coding/code_bounds.py: Move import into method

1f18999

mkoeppe changed the title ~~sage.coding: Doctest cosmetics, add # optional~~ sage.coding: Modularization fixes, doctest cosmetics, add # optional Jun 5, 2023

mkoeppe added the s: needs review label Jun 5, 2023

Matthias Koeppe added 2 commits June 5, 2023 12:08

sage.coding: More docstring cosmetics

1bc06a5

sage.coding: Even more docstring cosmetics

d6cacb8

mkoeppe requested a review from dimpase June 5, 2023 20:22

sage.coding: Final round of docstring cosmetics

45787c0

src/sage/coding/code_constructions.py: Make some docstrings raw

c039264

missing "`" added

f58dde7

sage.coding: More fixes to imports, # optional

d961aec

dcoudert suggested changes Jun 10, 2023

View reviewed changes

Matthias Koeppe added 2 commits June 10, 2023 08:40

sage.coding: Wrap some long lines

a67136a

Fix markup

5aac3bf

dcoudert approved these changes Jun 11, 2023

View reviewed changes

dcoudert removed the s: needs review label Jun 11, 2023

dcoudert added the s: positive review label Jun 11, 2023

vbraun merged commit dd8845d into sagemath:develop Jun 21, 2023

mkoeppe added this to the sage-10.1 milestone Jun 21, 2023

mkoeppe removed the s: positive review label Jun 21, 2023

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sage.coding: Modularization fixes, doctest cosmetics, add `# optional` #35729

sage.coding: Modularization fixes, doctest cosmetics, add `# optional` #35729

mkoeppe commented Jun 5, 2023 •

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sage.coding: Modularization fixes, doctest cosmetics, add # optional #35729

sage.coding: Modularization fixes, doctest cosmetics, add # optional #35729

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mkoeppe commented Jun 5, 2023 • edited Loading

📚 Description

📝 Checklist

⌛ Dependencies

dimpase commented Jun 6, 2023

mkoeppe commented Jun 6, 2023

dimpase commented Jun 7, 2023

mkoeppe commented Jun 7, 2023

dimpase commented Jun 7, 2023

mkoeppe commented Jun 7, 2023

dimpase commented Jun 7, 2023

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mkoeppe commented Jun 11, 2023

sage.coding: Modularization fixes, doctest cosmetics, add `# optional` #35729

sage.coding: Modularization fixes, doctest cosmetics, add `# optional` #35729

mkoeppe commented Jun 5, 2023 •

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