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AI-Generated Markdown Documentation#4307

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andrew-tawfeek wants to merge 55 commits into
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andrew-tawfeek:stable
Draft

AI-Generated Markdown Documentation#4307
andrew-tawfeek wants to merge 55 commits into
Macaulay2:developmentfrom
andrew-tawfeek:stable

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@andrew-tawfeek
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Description

Closes: None

The purpose of this pull request is to track/share with everyone the various Markdown files I'll be building around the M2 repository (with AI assistance, largely a mix of Claude Code and Codex). This is a draft pull request to encourage conversation, changes, and comments on the Markdown files being generated and edited.

This was started during the 2026 Workshop in Atlanta, GA. If you are here this week, please come talk to me about this in person if you have thoughts and/or changes you want me to make! I have followed the new draft pull request template found here.

AI Use

Please declare your use of AI on this pull request

  • [] I have not used AI
  • I have used AI

Extent of AI Usage:
Claude Code (Opus 4.7) and Codex (GPT 5.5)

AI Details:

Model(s) Used: Claude Opus 4.7 (xhigh effort) and GPT 5.5 (xhigh thinking)

AI Involvement Level:

  • Level 2: Superficial (Docstrings, regex, formatting)
  • Level 5: Structural (Algorithm logic, new functions)

How was AI used?
Markdown generation through strictly read-access to a clone of the M2 repository.

License

Choose one of the following

  • The code in this pull request is the public domain
  • The code in this pull request is licensed under GPLv2+
  • The code in this pull request is licensed under a GPLv2 compatible license (specify below)

@mahrud
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mahrud commented May 18, 2026

I'm a little confused about the purpose of this PR. Is it meant to be eventually merged, or just share what you've generated so far?

@andrew-tawfeek
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I'm a little confused about the purpose of this PR. Is it meant to be eventually merged, or just share what you've generated so far?

Largely the latter and to elicit feedback from (generally anyone) in the community about the contents of the markdown files. No more additional files are being generated though (diminishing returns, most internal sub-directories have a Markdown file covering its contents).

Ubuntu and others added 5 commits May 19, 2026 13:30
Relocates the generated Doxygen tree (html/ and xml/) plus the .nojekyll
marker and pages.yml workflow that uploads M2/BUILD/build/Macaulay2/docs/
doxygen/html as the Pages artifact. Titles were rewritten from
/home/ubuntu/M2-docs/... to /home/ubuntu/M2-web/... so that future
regen runs from this repo produce empty diffs.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Squashed import of the doxygen-comment work previously hosted in the
M2-docs companion repo (~641 small commits there, e.g. "Add class
doxygen for foo, bar, baz"). Strictly additive: 12,279 insertions
vs 521 deletions, where the deletions are trailing whitespace and a
handful of older one-line \ingroup directives folded into the new
file-level comment blocks. No semantic code changes.

Source: M2-docs (github.com/andrew-tawfeek/M2-docs) master @ e080fbdc15.
These comments are what populates https://atawfeek.com/M2-engine/docs/
when doxygen.sh regenerates against this tree.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…dule pins

Strips three non-documentation layers that had accumulated on stable so
that this branch's only diff vs Macaulay2/M2 development is the markdown
documentation added by the "Documentation additions" commits:

  - Reverts d2599fa: 313 .hpp/.cpp/.h/.c files restored to upstream
    versions (the Doxygen comment blocks now live on the doxygen branch).
  - Removes 213 CMake/ninja build artifacts under M2/BUILD/build/ that
    had been force-added past the directory's own .gitignore.
  - Resets the bdwgc, fflas_ffpack, flint, frobby, givaro submodule
    SHAs to match upstream/development.
  - Restores M2/Macaulay2/e/README.md to its pre-doxygen markdown form
    (clobbered as a side effect of the earlier cp -a in d2599fa).

Net diff vs upstream/development: only Documentation-additions markdown
(.md files) and their README modifications. The compiled Doxygen site
continues to deploy from the web branch; its C++ source of truth is now
the doxygen branch.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@andrew-tawfeek andrew-tawfeek changed the title Documentation of Structure of Macaulay2 AI-Generated Markdown Documentation May 20, 2026
Comment thread .github/workflows/pages.yml Outdated
@@ -0,0 +1,40 @@
name: Deploy Doxygen HTML to Pages
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Just to point out a lesson learned from a couple years back: adding doxygen documentation (and in particular updating it regularly) increases the size of the repository unreasonable (iirc at least like 50mb per update, since every single file seemed to be regenerated, so this quickly ballooned to a ~400mb repository which made cloning a pain)

@mahrud
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mahrud commented May 21, 2026

Also, just out of curiosity, how come some of the commits say "@andrew-tawfeek committed" and some say "Ubuntu committed"?

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2 participants