0f5ab27461f3397abf60177f3fb324a77f0bcf49
12 Commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
Tarik Moussa
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0f5ab27461 |
fix(citations): correct Kolpakov-Mednykh misattribution → Springborn 2008
arXiv:math/0603097 is Springborn 2008 ("A variational principle for weighted
Delaunay triangulations and hyperideal polyhedra"), not a Kolpakov-Mednykh paper.
The author pair Kolpakov & Mednykh has no joint publication from 2006; their
earliest collaboration is arXiv:1008.0312 (2010, on torus knots, unrelated).
The wrong author name was introduced during the Java→C++ port — the Java source
correctly links to math/0603097 without naming the authors; whoever ported it
invented "Kolpakov-Mednykh". The S1 citation audit (2026-05-31) then cemented
the error by adding the incorrect row to references.md.
Files corrected (7):
- code/include/hyper_ideal_utility.hpp
- code/include/hyper_ideal_functional.hpp
- code/tests/cgal/test_hyper_ideal_functional.cpp
- doc/math/references.md
- doc/roadmap/research-track.md
- doc/architecture/project-structure.md
- doc/api/tests.md
Also:
- doc/reviewer/math-derivation-citation-audit-2026-05-31.md: M1 post-correction noted
- doc/reviewer/finding-orchestration.md: lesson-learned section added (AI citation
audits can introduce plausible-but-wrong attributions; human expert review required
before CGAL submission)
- papers/MANUAL-DOWNLOAD.md: overview of papers requiring manual download (paywalled
journals, TU Berlin theses, books)
- .gitignore: papers/*.pdf excluded (downloaded arXiv PDFs, not tracked)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Tarik Moussa
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ba83974525 |
test: Java golden-value oracles for the five DCE math cores + P1-2/P1-3 fixes
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Add bit-for-bit (1e-12) golden-value oracle tests pinning the C++ pure-math and functional cores against the compiled upstream Java library (openjdk 17): - HyperIdealGoldenJava: Clausen/Л/ImLi2, ζ13/14/15/ζ, both tetrahedron-volume formulas (real de.varylab…Clausen / HyperIdealUtility). - EuclideanGoldenJava / SphericalGoldenJava: angle formulas + β relations + Л energy terms, plus FULL-MESH oracles driving the real EuclideanCyclicFunctional / SphericalFunctional on a shared tetrahedron — per-vertex gradient (Θ−Σα) and ΔE = E(x)−E(0) (C++ Gauss-Legendre path integral vs Java closed form). - SphericalGoldenJava.FullMeshEdgeDofGradient: edge-DOF gradient (vertex + edge components, α_opp⁺+α_opp⁻−θ_e) vs raw conformalEnergyAndGradient — locks Finding 3 at the solution level (audit items 4 & 5). - PeriodMatrix.NormalizeModulus_GoldenJava: τ-reduction fold convention vs the real DiscreteEllipticUtility.normalizeModulus (audit items 7 & 8). Subtlety documented: the spherical oracles call Java's raw conformalEnergyAndGradient, not evaluate() (which pre-runs a Brent gauge maximization that C++ factors into the Newton solver's spherical_gauge_shift). Also: - P1-2 (layout.hpp): Euclidean holonomy now uses a per-cut-edge rigid-motion fit g(z)=a·z+b, exposing residual_rotation = |arg(a)| as a diagnostic; non- regressive (flat case a=1 reduces to the old midpoint formula). - P1-3 (period_matrix.hpp): is_in_fundamental_domain fixed to the correct half-open SL(2,ℤ) domain (−½ ≤ Re < ½). Updated the now-exposed ComputePeriodMatrix_ReducedTau_InFD to assert the normalizeModulus domain (closed +½ edge) instead. Test counts (single source of truth = doc/api/tests.md): 272/272 pass, 0 skipped (26 non-CGAL + 246 CGAL). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> |
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Tarik Moussa
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a3ee9576d4 |
fix+test: Euclidean holonomy/τ end-to-end + spherical edge-DOF oracle (2026-05-29 audit)
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Bundles the 2026-05-29 Java↔C++ math-correctness audit (doc/reviewer/ java-port-audit.md, 11 findings) with two follow-up fixes. Audit code changes: - Finding 3 (spherical_functional): edge-DOF replacement parameterization via spher_eff_lambda; edge gradient α_opp⁺+α_opp⁻−θ_e (drops additive −(S⁺+S⁻)/2) - Finding 4 (spherical_hessian): always-compiled edge-DOF throw guard - Finding 6 (period_matrix): faithful normalizeModulus (0≤Re≤½, Im≥0, |τ|≥1) - Finding 9 (inversive_distance): degenerate-face limiting angles, no skip - Findings 1/2 (euclidean): degenerate gradient limiting angles + Hessian guard Euclidean holonomy/τ fix: develop the cut surface across the dual spanning tree only (cut_graph now exposes is_dual_tree), so genus-1 cut edges yield non-degenerate lattice generators. Previously τ came out 0 / NaN / 1e13 on the bundled tori; now matches the analytic revolution modulus i·√(R²−r²)/r. Re-enabled τ reporting in the Euclidean CLI; rewrote validation.md §3/§4 accordingly. Tests (240 CGAL, 0 skipped): - HolonomyEndToEnd ×3 — tori of revolution (4×4, hex 6×6, 8×8) vs analytic modulus - SphericalFunctional.EdgeGradient_RegularTetClosedForm — independent closed-form π/3 oracle locking the Finding-3 edge formula (the path-integral FD check cannot detect a wrong-but-conservative gradient) Also documents the latent spherical/hyperbolic holonomy-extraction bug (same single-development pattern, dead code today) in research-track.md (Phase 9c/10), and adds favour/normalisations to the codespell ignore list. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> |
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Tarik Moussa
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f25174ed69 |
feat: output_uv_map for InversiveDistance, error for CP-Euclidean, reviewer trio
Three reviewer-meeting deliverables in one commit.
(1) output_uv_map for the two remaining DCE entries
─────────────────────────────────────────────────
* Discrete_inversive_distance.h: full implementation. After Newton,
reconstruct effective Euclidean edge lengths from the converged
log-radii via the Bowers-Stephenson identity
`ℓᵢⱼ² = rᵢ² + rⱼ² + 2·Iᵢⱼ·rᵢ·rⱼ`, populate a temporary
EuclideanMaps with `lambda0 = log(ℓᵢⱼ²)`, and reuse the existing
`euclidean_layout(mesh, 0, eucl)` priority-BFS. Per-vertex
Point_2 coordinates written into the user-supplied pmap.
Optional `normalise_layout(true)` applies the canonical PCA
centroid + major-axis rotation, same as the other 3 entries.
* Discrete_circle_packing.h: throws std::runtime_error with a
clear pointer to Phase 9c rather than silently producing
nonsense. CP-Euclidean is face-based; the faithful output is a
per-face circle packing in ℝ², not a per-vertex Point_2 map.
A true layout requires BPS-2010 §6 (~150 lines, on the porting
roadmap as Phase 9c). Failing loudly is the honest default.
Tests: 2 new cases in test_cgal_phase8b_lite.cpp
(OutputUvMap_InversiveDistance_PopulatesPmap;
OutputUvMap_CPEuclidean_ThrowsClearly). Both green.
Suite total now 259 (was 257, +2). CGAL subtotal: 234 → 236.
(2) Reviewer meeting documents
──────────────────────────
New directory doc/reviewer/ with three files:
* briefing.md — one-page orientation for the reviewer.
What the project is, where to look first
(https://tmoussa.codeberg.page/ConformalLabpp/), the headline
evidence (tests/coverage/sanitizers/license), what we want from
them, what's deferred and why, and the 5 questions in a separate
file.
* questions.md — the 5 concrete decisions we want their second
opinion on:
Q1 Phase 9c (port-literal vs re-derive)
Q2 Phase 9b-analytic (worth ~2 weeks for ~6× speedup?)
Q3 CP-Euclidean output_uv_map (build now or defer?)
Q4 CGAL submission strategy (one package or five?)
Q5 geometry-central cross-validation co-authorship
Plus an explicit "what would you say no to?" question at the
bottom — negative feedback is the highest-value information.
* agenda.md — my own internal playbook (NOT to be sent).
60-min flow: 5-min thank-you, 10-min architecture tour,
30-min for Q1-Q5 in the order Q4-Q1-Q2-Q5-Q3, 5-min "no"
question, 5-min wrap-up. Includes post-meeting memo template
to fill out in the 30 min after.
* README.md — index for the directory; says which file goes
to whom and when to send.
(3) locked-vs-flexible.md known-limitations update
─────────────────────────────────────────────
"output_uv_map covers 3 of 5 entries" → "covers 4 of 5".
CP-Euclidean's throws-clearly behaviour documented as a Phase 9c
deliverable rather than a passive gap.
Bonus: extended .codespellrc ignore list (acknowledgement, the
British-English spelling I used in agenda.md).
Verifications on this commit:
259/259 tests pass (0 skipped)
scripts/check-test-counts.sh: OK (23 + 236 = 259)
scripts/quality/license-headers.sh: OK (66/66 SPDX)
python3 scripts/quality/cgal-conventions.py: OK (0/6 violations)
scripts/quality/codespell.sh: OK (0 typos)
scripts/quality/shellcheck.sh: OK (0 findings)
python3 scripts/check-markdown-links.py: OK (143/143)
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Tarik Moussa
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e04515c423 |
docs(doxygen): fix critical extraction bug; baseline 24% → 42% on public API
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>
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Tarik Moussa
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039cc26e36 |
Phase 8b-Lite: pipe-operator chaining for named parameters
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Adds `operator|` in `namespace CGAL` so package-local named parameters
can be combined left-to-right without modifying CGAL upstream:
auto p = CGAL::parameters::gradient_tolerance(1e-12)
| CGAL::parameters::max_iterations(500)
| CGAL::parameters::output_uv_map(uv);
CGAL::discrete_conformal_map_euclidean(mesh, p);
Why not the canonical `.a().b().c()` syntax
───────────────────────────────────────────
CGAL's standard chaining mechanism requires registering each named
parameter as a member function on `Named_function_parameters` via the
`CGAL_add_named_parameter` macro in
`CGAL/STL_Extension/internal/parameters_interface.h` — a vendored
upstream file that conformallab++ deliberately treats as read-only.
Adding member-function chainers for our package-local tags would
require either forking CGAL or modifying the vendored copy. Neither
is acceptable for a library that wants to remain portable across
future CGAL releases.
The pipe-operator achieves the same compositional semantics via a
free function in `namespace CGAL` (so ADL finds it for
`Named_function_parameters` operands). Implementation: rebuild the
right-hand-side `Named_function_parameters` with the left-hand-side
as its `Base`, producing an indistinguishable chain that every entry
function accepts unchanged.
Implementation: `code/include/CGAL/Conformal_map/internal/parameters.h`
lines 158-187. The operator is constrained to right-hand-sides with
`No_property` base (i.e. fresh single-parameter packs from the helper
functions), so it never collides with any future CGAL operator on the
same type.
Tests (2 new, total Phase-8b-Lite suite 15 → 17)
────────────────────────────────────────────────
* CGALPhase8bLite.NamedParamPipe_MultipleParamsTakeEffect
Chain three parameters; verify all three take effect (tight
tolerance respected + UV pmap populated + iteration cap honoured).
* CGALPhase8bLite.NamedParamPipe_TwoParams
Chain two parameters; verify max_iterations(0) blocks the loop
even when combined with another param.
Full CGAL suite: 234/234 PASSED, 0 SKIPPED (was 232).
Total: 257/257 PASSED, 0 SKIPPED (was 255).
scripts/check-test-counts.sh: OK.
Documentation updates
─────────────────────
* doc/tutorials/add-output-uv-map.md §3.4: "Current limitation: no
chaining" → "Chaining: use the pipe operator `|`". Explains why
CGAL's `.member()` syntax isn't available and shows the `|`
workaround with a working code example.
* doc/architecture/locked-vs-flexible.md §8: chaining now flagged as
shipped via pipe; recommended posture says `.member()` chaining
only if a user pushes for the CGAL-canonical syntax.
* doc/roadmap/porting-status.md §5: API limitations table updated.
* doc/api/tests.md: CGALPhase8bLite row 15 → 17, total 232 → 234.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Tarik Moussa
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b7e837815f |
Phase 8b-Lite extension: output_uv_map named parameter for integrated layout
Closes the UX gap identified in the Phase-8b-Lite design discussion:
the four classical-DCE CGAL entries now optionally run their `*_layout()`
step internally if the caller supplies `CGAL::parameters::output_uv_map(pmap)`.
Before this PR, the workflow was:
auto res = CGAL::discrete_conformal_map_euclidean(mesh);
// ... user has to re-set up maps, re-pin vertex, then ...
auto layout = euclidean_layout(mesh, res.x, maps);
// ... and copy coordinates into a property map manually.
After this PR:
auto uv = mesh.add_property_map<Vertex_index, K::Point_2>("uv", ...).first;
CGAL::discrete_conformal_map_euclidean(
mesh, CGAL::parameters::output_uv_map(uv));
// ... uv now populated for every vertex.
Coverage
────────
* `discrete_conformal_map_euclidean` — `Point_2` per vertex.
* `discrete_conformal_map_spherical` — `Point_3` per vertex (on S²).
* `discrete_conformal_map_hyper_ideal` — `Point_2` per vertex (Poincaré disk).
CP-Euclidean and Inversive-Distance entries do not yet support
`output_uv_map` — face-based packing has no per-vertex UV concept, and
inversive-distance needs a dedicated layout routine that uses Luo's
edge-length formula (planned follow-up).
New named parameters (`code/include/CGAL/Conformal_map/internal/parameters.h`)
─────────────────────────────────────────────────────────────────────────────
* `output_uv_map(pmap)` — write coordinates into pmap after layout.
* `normalise_layout(bool)` — apply post-layout canonical normalisation
(PCA centroid for Euclidean, north-pole alignment for Spherical,
Möbius centring for Hyper-ideal).
Both follow the existing Phase-8a-MVP named-parameter convention.
Chained syntax (`.output_uv_map(...).normalise_layout(true)`) is not
yet supported — pass them one at a time.
Tests (5 new in test_cgal_phase8b_lite.cpp)
───────────────────────────────────────────
* `OutputUvMap_Euclidean_PopulatesPmap` — UVs are finite + non-trivial.
* `OutputUvMap_Spherical_PopulatesXyz` — every output on unit S².
* `OutputUvMap_HyperIdeal_PointsInPoincareDisk` — |p|² ≤ 1 if converged.
* `OutputUvMap_Absent_DoesNotRunLayout` — no parameter ⇒ no layout.
* `OutputUvMap_NormaliseLayout_TakesEffect` — both raw + norm calls
return finite UVs (named-parameter chaining limitation documented).
All five pass. Full CGAL suite: 232/232, 0 skipped (was 227).
doc/api/tests.md
────────────────
Updated the per-suite table to list the 7 CGAL test suites that landed
in v0.9.0 (8a MVP + 9a + 9b + 8b-Lite) but had not yet been added to the
canonical table. Total: 227 → 232. This brings the doc back in sync
with `ctest` output and unblocks future `scripts/check-test-counts.sh`
runs.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Tarik Moussa
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540f71a629 |
release: v0.9.0 — finalise PR #11 with CHANGELOG, version bump, stub cleanup
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> |
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Tarik Moussa
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52f61cec36 |
Update all doc test counts to 176 CGAL tests, 0 skipped
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> |
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Tarik Moussa
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88a99d8bd1 |
fix: correct 16 inconsistencies found by consistency audit
Math / code: - layout.hpp: add explanatory comment for Möbius deck transformation (from_three with z1=w1, z2=w2 encodes T fixing cut-edge endpoints) - layout.hpp: document spherical holonomy limitation — Vector2d stores only (x,y) of 3-D position diff; full SO(3) representation deferred Gradient sign convention (CLAUDE.md was wrong): - Euclidean and Spherical both use G_v = Θ_v − actual (target minus actual) - HyperIdeal uses G_v = actual − Θ_v - Hessian sign differs: Euclidean PSD, Spherical NSD → −H, HyperIdeal PSD Test counts (were inconsistent across all files): - Actual: 176 CGAL tests, 2 GTEST_SKIP (not 173/170/174, not 1 skip) - The 2 skips are EuclideanFunctional + SphericalFunctional Hessian gradient checks (Java @Ignore ports) — not HyperIdeal Hessian as previously stated - doc/api/tests.md: add missing SmokeEuclidean suite (3 tests), EuclideanLayout (2), SphericalLayout (1), fix GaussBonnet 8→12, MeshIO 9→6, Layout 8→6, EuclideanFunctional 11→12, HomologyGenerators no longer a GTEST_SKIP stub (live test on brezel2.obj) - doc/roadmap/phases.md: Phase 7 cumulative 158→176 tests - doc/roadmap/phases.md: Phase 3 clarified — HyperIdeal Hessian is FD - CLAUDE.md: suite count 28→34, test ref 173+36→174+36 - scripts/try_it.sh: expected output 173/1 skipped → 174/2 skipped CI table (CLAUDE.md): - test-cgal now triggers on pull requests only (not main/dev pushes) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> |
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Tarik Moussa
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e28aee7051 |
docs: Mathematiker-Onboarding — Theorie, Validierung, Beispiel-Meshes, 170 Tests
Ziel: einem interessierten Mathematiker ermöglichen, die bisherige Arbeit
unabhängig zu validieren und eigene Forschung beizutragen.
Neu:
doc/math/discrete-conformal-theory.md
Kompakte mathematische Einführung (DCE, Variationsprinzip, drei
Geometriemodi, Holonomie, Periodenmatrix) für Riemann-Flächen-Kenner.
doc/math/validation.md
Analytisch bekannte Sollwerte + wie man sie mit dem Code prüft:
Gauss–Bonnet (χ), τ ∈ Fundamentaldomäne (3 Invarianten), Symmetrie-
Argumente für τ=i (4-fach) und τ=e^{iπ/3} (6-fach), Newton-Konvergenz,
Gradienten-Check (FD), Holonomie-Kommutator. Reviewer-Checkliste.
CONTRIBUTING.md (Root)
Gitea/GitHub-Standard: CONTRIBUTING.md im Root-Verzeichnis als
Kurzreferenz mit Links zu doc/contributing.md und den Math-Docs.
code/data/off/torus_4x4.off — 16 Vertices, 32 Flächen, Genus 1
code/data/off/torus_8x8.off — 64 Vertices, 128 Flächen, Genus 1
code/data/off/torus_hex_6x6.off — 36 Vertices, 72 Flächen, 6-fach Sym.
Aktualisiert:
README.md — 158 → 170 Tests, zwei neue Math-Links in Tabelle
doc/api/tests.md — 28 Suiten, 170 Tests, 1 Skip (korrigiert)
doc/contributing.md — Testzähler 158+2 → 170+1
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Tarik Moussa
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95d48c434a |
chore: .gitignore + vergessene Doc-Dateien nachgetragen
.gitignore: build-Verzeichnisse, .DS_Store, .claude/, CMake-Artefakte Doc-Dateien die beim Restructure-Commit fehlten: doc/api/headers.md — alle 24 Public-Header mit Beschreibung doc/api/tests.md — 26 Suiten, 158 Tests, Einzelzahlen doc/architecture/design-decisions.md — Architekturentscheidungen + Begründung doc/architecture/project-structure.md — Verzeichnisbaum + Build-Targets README.md: Links zu den vier neuen Doc-Dateien ergänzt Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> |