sage.coding: Modularization fixes, doctest cosmetics, add `# optional` by mkoeppe · Pull Request #35729 · sagemath/sage

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



-    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!

Matthias Koeppe added 7 commits June 4, 2023 23:14

sage.coding: Doctest cosmetics, add # optional

6d3bc3e

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

sage.coding: More docstring cosmetics

1bc06a5

sage.coding: Even more docstring cosmetics

d6cacb8

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 requested 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 added s: positive review and removed s: needs review labels Jun 11, 2023

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



		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

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📚 Description

📝 Checklist

⌛ Dependencies

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dimpase commented Jun 6, 2023

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