ROOT CAUSE FIX
The Doxyfile EXCLUDE_PATTERNS line contained `*/* 2.hpp` (note the
space — a stray glob from macOS-style "foo 2.hpp" duplicate files).
That pattern was silently matching ALL .hpp / .h files, so Doxygen was
indexing nothing under code/include/. The pre-existing 556 KB of HTML
output was effectively documenting only README.md, CLAUDE.md and a
small stub for std:: — not the C++ API at all.
After fixing the pattern (and properly escaping the space-prefixed
"foo 2.hpp / foo 2.h" macOS-dup patterns), Doxygen now extracts 141
compounds and emits 248 HTML pages from the public headers.
WHAT THIS PR ADDS
1. Doxyfile fix: correct EXCLUDE_PATTERNS; add GENERATE_XML for the
coverage measurement script; add MathJax for `$$...$$` math in
markdown; add the missing CGAL `\cgalParamNBegin/End/Description/
Default/...` aliases so CGAL-style param blocks render correctly.
2. New headers:
- code/include/CGAL/Conformal_map/doxygen_groups.h
defines `PkgConformalMap{,Ref,Concepts,NamedParameters}`,
resolving 17 prior "non-existing group" warnings.
- code/include/CGAL/Conformal_map/doxygen_namespaces.h
gives every namespace under `CGAL::` and `conformallab::` a
brief description.
3. New tool: scripts/doxygen-coverage.sh
Parses the XML output and reports % of public symbols (excluding
the `detail::` implementation namespaces by default) that have a
non-empty brief/detailed description. Supports `--list-undoc`
and `--threshold N` for CI integration.
4. Substantial docstring additions to the public CGAL headers:
`Conformal_map_traits.h`, `Discrete_circle_packing.h`,
`Discrete_inversive_distance.h`, `conformal_mesh.hpp`,
`Discrete_conformal_map.h` (Hyper_ideal_map_result fields).
5. Markdown housekeeping that the strict-warning Doxygen run surfaced:
tests.md (escape literal `#` in table cell),
locked-vs-flexible.md (broken section anchor),
overall_pipeline.md (replace `$$LaTeX$$` with inline-unicode math).
CURRENT NUMBERS
before: ~24% documented (public API; the prior "87%" claim was
based on the broken extraction)
after: 42% documented (165 of 396 public symbols)
warnings: 0 (was 27 spurious + a flood of bogus undocumented
warnings hidden by the buggy EXCLUDE pattern)
NEXT (in a follow-up commit on this branch)
The remaining 231 public symbols (mostly in `layout.hpp`,
`hyper_ideal_functional.hpp`, `spherical_functional.hpp`, the per-mode
functional/Hessian files) can be brought to ~100% with another pass of
short `///` brief descriptions. The coverage script is the gate; CI
can begin enforcing `--threshold 95` once the next pass lands.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Doxygen now builds with **0 warnings** (was 27).
Root cause: `[label](doc/api/tests.md)`-style relative markdown links in
README.md and CLAUDE.md were being interpreted by Doxygen as \ref
commands and failed to resolve (Doxygen indexes .md files by basename,
not by repo-relative path).
Fix: add a per-file `FILTER_PATTERNS` to Doxyfile that rewrites
`[label](path/to/file.md)` into `<a href="path/to/file.md">label</a>`
just for Doxygen. HTML anchors bypass \ref resolution entirely; the
generated Doxygen HTML still hyperlinks correctly. The on-disk
markdown is untouched, so GitHub rendering is unaffected.
New file: scripts/doxygen-md-filter.sh (24 lines, documented).
Also: append a "Known limitations (state at the time of the reviewer
meeting)" table to doc/architecture/locked-vs-flexible.md so the
external reviewer sees the 7 deliberate gaps (output_uv_map covers
3 of 5 entries; pipe-only chaining; Phase 9b-analytic derived but not
implemented; Doxygen WARN_IF_UNDOCUMENTED policy; CI test-count gate;
research-track utilities) with effort estimates next to each.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Two complementary improvements aimed at reducing recurring maintenance
overhead:
1. **Test-count centralisation** — `doc/api/tests.md` is now the
single source of truth for the test counts. All other docs
(README, CLAUDE.md, doc/contributing.md, doc/getting-started.md,
doc/math/validation.md, doc/math/validation-protocol.md,
scripts/try_it.sh) use qualitative phrasing + a link instead of
hardcoded numbers. The previous regime had eight places with
"227 CGAL tests, 23 non-CGAL tests" that drifted apart across
releases (the v0.9.0 release-prep needed to touch nine files).
2. **Versioning policy** — `doc/release-policy.md` (new, ~250 lines)
formalises:
* SemVer rules for the pre-1.0 and post-1.0 phases.
* Phase-milestone → MINOR-bump mapping (v0.10.0 → Phase 9c, …).
* Single-source-of-truth table for moving numbers (test counts,
version, date).
* Step-by-step release process (the recipe that worked for v0.9.0
after the false-start with PR #11/#12).
* Hotfix policy + post-1.0 deprecation policy.
* Known failure modes and how to recover from them.
Plus a small CI gate:
3. **scripts/check-test-counts.sh** — verifies the totals in
doc/api/tests.md match `ctest` output. Re-uses existing build-cgal/
if present. Exit 0 on match, 1 on divergence with recovery hints.
Cheap enough (~30 s) to run on every PR.
Other cleanups
──────────────
* code/tests/cgal/CMakeLists.txt — stale "Test 7 (genus-2 homology)
as GTEST_SKIP stub until Phase 8" comment removed; that test landed
as HomologyGenerators.Genus2_FourCutEdges in Phase 7.
* CLAUDE.md — "test-fast also runs stubs" Known Quirks entry updated
to reflect the v0.9.0 stub cleanup (no GTEST_SKIPs remain).
* CLAUDE.md doc map — new entry for doc/release-policy.md.
Stubs audit
───────────
Zero GTEST_SKIP() calls remain in the codebase as of this commit.
The only references to stubs are in historical documentation
(CHANGELOG.md v0.7.0 entry, doc/roadmap/* "deferred to research-track"
notes) — those are intended.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Closes the v0.9.0 release loop on top of Phase 9a-Newton + Phase 8b-Lite:
* CHANGELOG.md (NEW) — Keep-A-Changelog format, with v0.9.0 entry
detailing all Phase 9a / 9b / 8b-Lite contents and the doc-audit
corrections that landed via PR #10.
* CITATION.cff — version 0.7.0 → 0.9.0, date 2026-05-18 → 2026-05-22.
* Stale HDS-port stubs removed (13 GTEST_SKIPs total):
- code/tests/test_spherical_functional.cpp
- code/tests/test_hyper_ideal_functional.cpp
- code/tests/test_hyper_ideal_hyperelliptic_utility.cpp
These referenced a "HDS port (Phase 4)" that never happened —
CoHDS was intentionally replaced by CGAL::Surface_mesh, and the
functional tests live in code/tests/cgal/test_*_functional.cpp.
* Test-count updates everywhere:
- Non-CGAL 36 → 23 (drop = 13 deleted stubs)
- CGAL 176 → 227
- Total 212 → 250 (+38 net, 0 skipped)
Files: README.md, CLAUDE.md, CHANGELOG.md, scripts/try_it.sh,
doc/api/tests.md, doc/contributing.md, doc/getting-started.md,
doc/math/validation.md.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Propagates the new baseline (176 passed, 0 skipped) established by the
GradientCheck_Hessian implementation across all documentation files that
previously referenced the stale counts (174/173/170 + 1-2 skips).
Files updated: CLAUDE.md, doc/api/tests.md, doc/contributing.md,
doc/getting-started.md, doc/math/novelty-statement.md,
doc/math/validation.md, doc/math/validation-protocol.md, scripts/try_it.sh
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
