Update Sphinx/Doxygen/Breathe docs: pin latest deps, fix config, expand API coverage

[Copilot]

• Analyze branch history and understand the original goal (Sphinx/Doxygen/Breathe documentation framework)
• Reset working tree to match main exactly (per reviewer request)
• Re-apply docs/ directory as the only addition on top of main
• Remove files from old branch that don't exist on main
• Fix docs for current codebase: correct version (0.1.0), class name (layer_sentry), macro (PHLEX_DETAIL_REGISTER_PLUGIN)
• Pin latest dependency versions (sphinx 9.1, breathe 4.36, sphinx-rtd-theme 3.1)
• Add .gitignore entries for docs build output (docs/doxygen/, docs/build/)
• Add module docstring to conf.py for ruff D100 compliance
• Code review
• Security scan (8 pre-existing alerts in workflow files; none from this PR)

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[greenc-FNAL]

@copilot I think for maximum clarity, it would be better to reset this branch to upstream/main and then re-do the work following the current philosophy, functions/class structure, etc.

[Copilot]

@copilot I think for maximum clarity, it would be better to reset this branch to upstream/main and then re-do the work following the current philosophy, functions/class structure, etc.

Done. In commit 412a5ec I reset the branch to main and removed all the stale files from the old base. In 0712ae9 I fixed the docs to match the current codebase (correct class names, macros, version).

The PR now shows only 13 files changed (135 additions, 0 deletions from main): the docs/ directory with Sphinx/Doxygen/Breathe configuration and API pages, plus .gitignore entries for docs build output.

[Copilot]

Pull request overview

Adds a Sphinx + Doxygen + Breathe documentation scaffold under docs/ to generate API reference documentation for key phlex::experimental types, along with dependency requirements and gitignore entries for generated outputs.

Changes:

• Add Sphinx project entrypoint (index.rst) and minimal conf.py wired to Breathe.
• Add API reference .rst pages for several phlex::experimental classes.
• Add Doxygen configuration + Python requirements, and ignore generated docs artifacts in .gitignore.

Reviewed changes

Copilot reviewed 12 out of 13 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
docs/source/index.rst	Adds top-level Sphinx landing page and toctree for API pages.
docs/source/conf.py	Adds Sphinx configuration with Breathe integration.
docs/source/api/graph_proxy.rst	Adds API page for phlex::experimental::graph_proxy.
docs/source/api/framework_graph.rst	Adds API page for framework_graph and layer_sentry.
docs/source/api/registrar.rst	Adds API page for phlex::experimental::registrar.
docs/source/api/declared_transform.rst	Adds API page for declared_transform.
docs/source/api/declared_fold.rst	Adds API page for declared_fold.
docs/source/api/declared_unfold.rst	Adds API page for declared_unfold.
docs/source/api/product_store.rst	Adds API page for product_store.
docs/source/api/products.rst	Adds API page for products.
docs/requirements.txt	Adds Python dependencies for building docs.
docs/Doxyfile	Adds Doxygen configuration to emit XML for Breathe.
.gitignore	Ignores generated Doxygen/Sphinx build output directories.

Comments suppressed due to low confidence (1)

docs/requirements.txt:4

• The PR description says dependencies are “pinned”, but requirements.txt uses version ranges (e.g., >=9.1,<10) which will allow new releases and can change doc build output over time. Either pin exact versions (e.g., ==...) to match the description, or update the description to reflect that these are minimum/compatible ranges. Also remove the trailing blank line at EOF to avoid generating a 4th empty requirement line.

sphinx>=9.1,<10
breathe>=4.36,<5
sphinx-rtd-theme>=3.1,<4

[greenc-FNAL]

@phlexbot python-fix

[github-actions]

Automatic ruff fixes pushed (commit af87c94).
⚠️ Note: Some issues may require manual review and fixing.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

@@            Coverage Diff             @@
##             main     #323      +/-   ##
==========================================
+ Coverage   82.26%   82.36%   +0.09%     
==========================================
  Files         127      127              
  Lines        3102     3102              
  Branches      547      547              
==========================================
+ Hits         2552     2555       +3     
  Misses        333      333              
+ Partials      217      214       -3     

Flag	Coverage Δ
unittests	82.36% <ø> (+0.09%)	⬆️

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see 3 files with indirect coverage changes

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