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>
doc/api/headers.md — all 24 public headers with descriptions
doc/api/tests.md — 26 test suites, individual counts, run instructions
doc/architecture/design-decisions.md — 5 key design choices with rationale
doc/architecture/project-structure.md — full directory tree + build targets
README + overall_pipeline.md link tables updated.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
README.md: reduced from 703 to ~75 lines — what/why, status, quick
start, minimal usage example, navigation table to doc/ files.
doc/architecture/overall_pipeline.md: trimmed — roadmap, extension
points, declarative pipeline YAML, and references sections removed
(each now has its own dedicated file). Replaced with a link table.
New files:
doc/getting-started.md — build modes, single-test invocation, CLI
doc/api/pipeline.md — full pipeline API with code for all 3 geometries
doc/api/extending.md — new functionals, geometry modes, Java porting guide
doc/api/contracts.md — processing unit preconditions/provides table
doc/api/cgal-package.md — Phase 8 CGAL package design + YAML pipeline (TODO)
doc/math/geometry-modes.md — Euclidean/Spherical/HyperIdeal comparison
doc/math/references.md — all papers by module
doc/roadmap/phases.md — Phases 1–10 with porting/research boundary
doc/roadmap/java-parity.md — Java vs C++ feature parity table
doc/contributing.md — language policy, test standards, release flow
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Structured the development roadmap into four blocks with an explicit
boundary marker separating direct Java ports (Phase 1–7) from
infrastructure (Phase 8), remaining porting (Phase 9), and new
research territory (Phase 10+).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
README:
- Neuer Einstieg mit vollständiger Dissertation-Referenz (Titel, TU Berlin 2016,
DOI 10.14279/depositonce-5415, CC BY-SA 4.0)
- Links zu Original-Java-Repo, sechel.de und linkedin.com/in/sechel
- Neuer Abschnitt "Ursprung & Danksagung" vor der Lizenz
doc/architecture/overall_pipeline.md:
- Neuer "Origin"-Abschnitt ganz oben mit vollständiger Quellenangabe
- Literaturabschnitt erweitert: Dissertation als "Primary source" hervorgehoben,
Java-Original-Repo als direkter Port-Bezug dokumentiert
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Ersetzt den generischen Geometry-Framework-Entwurf durch eine präzise
Beschreibung der tatsächlichen konformen Geometrie-Pipeline:
- Klare Positionierung: spezialisiertes Werkzeug für diskrete konforme
Abbildungen, kein generisches Mesh-Processing-Framework
- Korrigiertes Mermaid-Diagramm: alle 3 Phasen mit realen Komponenten
(load_mesh → setup_maps → GB-check → Newton → CutGraph → Layout →
halfedge_uv → Holonomie → Periodenmatrix → Fundamentalbereich → Export)
- Preconditions/Capabilities-Tabelle für alle Processing-Units
- Drei Geometrie-Modi (Euklidisch/Sphärisch/Hyper-ideal) im Vergleich
- MobiusMap, halfedge_uv, Priority-BFS, SL(2,ℤ)-Reduktion dokumentiert
- Realistischer YAML-Pipeline-Entwurf als Phase-8-Ziel (Tokens statt Prosa)
- Erweiterungspunkte: neues Funktional, neue Geometrie, neues Unit
- Alle Literaturverweise direkt auf Implementierungsstellen gemappt
- "Nice To Have but maybe too much" komplett entfernt
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
