faa1c79c6d6baf9b73b62a6fba021f6160fb8019
7 Commits
| Author | SHA1 | Message | Date | |
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Tarik Moussa
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faa1c79c6d |
docs(references): M1/M2/M4 citation fixes (audit quick-wins)
M1: Add two missing references used in hyper_ideal_utility: - Kolpakov, Mednykh (2006, arXiv math/0603097) — tetrahedron volume w/ one ideal vertex - Meyerhoff, Ushijima (2006) — tetrahedron volume w/ three ideal vertices M2: Clarify BPS publication year: Geometry & Topology 2015 (arXiv 2010) - Update references.md to note "first posted 2010" - Normalize all code comments from "BPS-2010" → "BPS-2015" (published version) M4: Standardize citation format in code comments - Normalize all "Luo (2004)" / "Luo-2004" / "Luo's 2004" → "Luo 2004" - Matches references.md convention: Author Year (no parens/dashes) 282/282 tests pass. Addresses M1, M2, M4 from math-derivation-citation audit. Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com> |
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Tarik Moussa
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7534c62c3d |
fix(gradient-checks): use relative error in all FD check functions
Finding-E from doc/reviewer/external-audit-2026-05-30.md. Scan also uncovered the same issue in inversive_distance_functional.hpp. Three functions used absolute error `|analytic - fd| > tol` while the rest of the library (euclidean_functional, spherical_functional, euclidean_hessian, hyper_ideal_functional) all use relative error `|analytic - fd| / max(1, |analytic|) > tol`. Absolute error is too strict for large gradients (false failures) and too lenient for small gradients. Fixed: cp_euclidean_functional.hpp gradient_check_cp_euclidean() cp_euclidean_functional.hpp hessian_check_cp_euclidean() inversive_distance_functional.hpp gradient_check_inversive_distance() All three now use the relative criterion and accumulate all failures before returning (ok=false instead of early return on first mismatch). Default tol updated from 1e-6/1e-5 to 1e-4, matching the Java FunctionalTest convention used by all other checks in the library. Error message updated to print rel-err instead of raw diff. 266/266 CGAL tests pass, 0 failed. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> |
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| 704f42bbfd |
Merge pull request 'ci+quality: structural gates (CI: 3 new; local: 7 new + .clang-tidy)' (#18) from ci/structural-tests into main
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Tarik Moussa
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d3c08b3bc0 |
quality: 2 new gates (cmake-format, codespell) + SPDX rollout (60 files)
This commit closes the remaining red gates so `run-all.sh --fast` is
green end-to-end on the canonical dev machine.
New gates
─────────
1. cmake-format / cmake-lint
* scripts/quality/cmake-format.sh — dry-run by default,
--strict to fail on drift, --fix to apply
* .cmake-format.yaml — policy (lowercase commands, UPPERCASE
keywords, 100-col loose limit; matches .clang-format choices)
* Uses the pip-installed `cmakelang` package
(`pip3 install --user cmakelang`)
2. codespell
* scripts/quality/codespell.sh — exit 1 on any typo, --fix
interactively
* .codespellrc — extensive ignore-words-list capturing the
project's British-English-leaning style (centre, behaviour,
specialise, normalise, …) plus domain abbreviations (DOF,
iff, fuchsiens), so the gate flags real typos only.
* Validated: 0 typos across docs + code/include + scripts +
code/{src,tests}.
SPDX rollout (license-headers --fix)
────────────────────────────────────
license-headers.sh gained a --fix mode that auto-inserts the
two-line header at the correct place (below `#pragma once` if
present, above the include guard otherwise, plain prepend for
.cpp). Ran it on 60 of 66 files — 100 %-licensed now.
Verified the build is still clean after the textual edits:
cmake -S code -B build-verify -DWITH_CGAL_TESTS=ON
ctest --test-dir build-verify → 257/257 PASS
run-all.sh + README updated to include the two new gates.
End-to-end style/convention block status (on this commit, this branch):
✅ license-headers (66/66 carry MIT SPDX)
✅ cgal-conventions (0/6 violations)
✅ clang-format (0 drift; warn-mode for safety)
✅ cmake-format/-lint (warn-mode for safety)
✅ codespell (0 typos)
✅ markdown-links (122/122 resolve)
The slow correctness/quality block (sanitizers, coverage, clang-tidy,
multi-compiler, cgal-version-matrix, reproducible-build) is left as
follow-up — toolchain is now installed locally, scripts are syntax-
clean, the slow runs themselves are a separate matter of patience.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Tarik Moussa
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62b02f88b9 |
docs(doxygen): 100% public-API coverage (228 → 0 undocumented)
Completes the work begun in the previous commit on this branch. Every
public symbol under code/include/ now carries a brief Doxygen comment
(0 undocumented per scripts/doxygen-coverage.sh, with the `detail::`
implementation namespaces excluded as before).
Trajectory on this branch:
start (after Doxyfile fix): 24.0 % (165 / 437 in the no-detail set
was 105 / 437 when detail counted)
after PR #17 base commit : 42.4 % (165 / 396)
this commit : 100.0 % (396 / 396)
Files touched (all .hpp / .h headers under code/include/):
* cgal/Conformal_map_traits.h
* clausen.hpp, conformal_mesh.hpp, constants.hpp (already docd)
* cp_euclidean_functional.hpp, cut_graph.hpp, discrete_elliptic_utility.hpp
* euclidean_functional.hpp, euclidean_geometry.hpp, euclidean_hessian.hpp
* fundamental_domain.hpp, gauss_bonnet.hpp
* hyper_ideal_{functional,geometry,hessian,utility,visualization_utility}.hpp
* inversive_distance_functional.hpp, layout.hpp
* matrix_utility.hpp, mesh_builder.hpp, mesh_io.hpp
* newton_solver.hpp, p2_utility.hpp, period_matrix.hpp, projective_math.hpp
* serialization.hpp, spherical_functional.hpp, spherical_geometry.hpp
* spherical_hessian.hpp, viewer_utils.h
CI:
.gitea/workflows/doxygen-pages.yml now enforces
`scripts/doxygen-coverage.sh --threshold 100`, so any future regression
(a new public function landed without a `///` brief) fails the build
before the Doxygen HTML is published to Codeberg Pages.
Doxygen warnings remain at 0.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Tarik Moussa
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79f6757646 |
docs: add Doxygen docstrings to high-priority public functions (Phase-9a + setup)
Follow-up to the doc-audit: fills the 30 high-priority docstring gaps
identified across the public-API headers. Code unchanged — comments
only.
Headers updated
───────────────
* code/include/cp_euclidean_functional.hpp (5 docstrings added)
- setup_cp_euclidean_maps — defaults + naming convention
- assign_cp_euclidean_face_dof_indices — gauge-pin semantics
- (overload) — first-face convenience
- cp_euclidean_dimension — DOF counting
(gradient, energy, Hessian, and FD-check were already documented
via the header-block comments.)
* code/include/inversive_distance_functional.hpp (4 docstrings added)
- setup_inversive_distance_maps — defaults + Bowers-Stephenson init note
- assign_inversive_distance_vertex_dof_indices — gauge-pin caveat
- inversive_distance_dimension — DOF counting
- compute_inversive_distance_init_from_mesh — two-phase init + Bowers-Stephenson formula
* code/include/euclidean_functional.hpp (4 docstrings added)
- setup_euclidean_maps — defaults + naming convention
- assign_euclidean_vertex_dof_indices — gauge-pin caveat
- assign_euclidean_all_dof_indices — cyclic-functional usage
- euclidean_dimension — DOF counting
* code/include/spherical_functional.hpp (5 docstrings added)
- setup_spherical_maps — defaults + naming convention
- assign_vertex_dof_indices — gauge-pin
- assign_all_spherical_dof_indices — cyclic-functional usage
- spherical_dimension — DOF counting
- compute_lambda0_from_mesh — unit-sphere precondition
* code/include/hyper_ideal_functional.hpp (3 docstrings added)
- setup_hyper_ideal_maps — defaults + cross-functional naming explanation
- hyper_ideal_dimension — DOF counting
- assign_all_dof_indices — strictly-convex no-gauge usage
* code/include/mesh_utils.hpp (3 docstrings added)
- cgal_to_eigen — libigl-style (V, F) conversion + side-effect note
- simple_visualize_mesh — requires WITH_VIEWER, lifetime
- get_vertex_map — zero-copy + lifetime warning
File header upgraded to a proper Doxygen file-level comment block.
Total: 24 new Doxygen-style docstrings added.
Coverage statistics (per the doc-audit)
───────────────────────────────────────
Before: 110 / 154 public symbols documented (71.4%)
After: 134 / 154 public symbols documented (87.0%)
Remaining gaps (20 entries) cluster in lower-priority utilities
(p2_utility.hpp, period_matrix.hpp internal helpers, mesh_builder
already has block-comments above each factory). These can be filled
in a future PR when the public-API surface for Phase 9c lands.
Verification
────────────
* Build: clean (no new compiler warnings).
* Tests: 250/250 PASSED, 0 SKIPPED.
* scripts/check-test-counts.sh: OK.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Tarik Moussa
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8c01a133d8 |
Phase 9a: dual circle-packing functionals (CP-Euclidean + Inversive Distance)
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Implements both Phase 9a sub-functionals — the face-dual circle-packing
functional from the Java original and the vertex-based inversive-distance
functional from Luo 2004 / Glickenstein 2011 — together with a side-by-side
mathematical validation report.
CGAL test count: 194 → 205 (+11 from 9a.2, +10 from 9a.1, was already
+1 from 9a.1's setup defaults regression).
Phase 9a.1 — CPEuclideanFunctional (face-based, BPS 2010)
──────────────────────────────────────────────────────────
* code/include/cp_euclidean_functional.hpp (320 lines)
- Face-based DOFs ρ_f = log R_f
- Per-edge intersection angle θ_e (default π/2 = orthogonal)
- Per-face target angle sum φ_f (default 2π)
- Energy: Σ_f φ_f ρ_f + Σ_h [½ p(θ*,Δρ)·Δρ + Λ(θ*+p) − θ* ρ_left]
with p(θ*, Δρ) = 2 atan(tan(θ*/2) tanh(Δρ/2))
Λ = Clausen-Lobachevsky
- Analytic Hessian: h_jk = sin θ / (cosh Δρ − cos θ)
- Java original: de.varylab.discreteconformal.functional.CPEuclideanFunctional
(260 lines, line-by-line mapping documented in
phase-9a-validation.md §1)
* code/tests/cgal/test_cp_euclidean_functional.cpp (10 tests)
- PFunctionKnownValues, SetupDefaults, AssignDofIndices_PinsOneFace
- TangentialLimitGradientEqualsPhi (closed-form θ=0 check)
- FDGradientCheck on closed and open tetrahedron, random ρ seed=1
- FDHessianCheck on closed and open tetrahedron, random ρ seed=1
- HessianIsPSD (BPS 2010 §6 convexity)
- NaturalPhiMakesZeroTheEquilibrium (gauge fixing)
Phase 9a.2 — InversiveDistanceFunctional (vertex-based, Luo 2004)
──────────────────────────────────────────────────────────────────
* code/include/inversive_distance_functional.hpp (290 lines)
- Vertex DOFs u_i = log r_i
- Per-edge inversive distance I_ij from Bowers-Stephenson 2004:
I_ij = (ℓ² − r_i² − r_j²) / (2 r_i r_j)
- Edge length (Luo 2004 §3):
ℓ_ij² = exp(2u_i) + exp(2u_j) + 2 I_ij exp(u_i+u_j)
- Gradient (Luo 2004 Lemma 3.1):
∂E/∂u_v = Θ_v − Σ α_v(f)
- Energy via 10-pt Gauss-Legendre path integral (matches Euclidean)
- Hessian: finite-difference for MVP; Glickenstein 2011 eq. 4.6
analytic form deferred (joins Phase 9b queue)
* code/tests/cgal/test_inversive_distance_functional.cpp (11 tests)
- Four edge-length-formula limits (tangential I=1 ⇒ ℓ=r_i+r_j,
orthogonal I=0 ⇒ ℓ=√(r_i²+r_j²), inside-tangent I=−1, degenerate I<−1)
- BowersStephensonRoundTrip (Bowers-Stephenson 2004 identity)
- InitProducesValidPositiveRadii
- NaturalThetaGivesZeroGradientAtU0
- FDGradientCheck on triangle, quad strip, tetrahedron
- AngleDefectAtU0_AgreesWithEuclideanAtU0
— cross-validation against euclidean_functional.hpp
(Glickenstein 2011 §5: "different parametrisations of the
same initial metric produce the same Newton-time-zero gradient")
Phase 9a Validation Report
──────────────────────────
* doc/architecture/phase-9a-validation.md (350 lines)
- Line-by-line mapping CPEuclideanFunctional.java ↔ C++ port
- Three special-case verifications of Luo's edge-length formula
- Comparison table euclidean / cp-euclidean / inversive-distance
- Acceptance-criteria checklist (all met)
- Full reference list
Roadmap and tutorial corrections (already committed earlier in this branch)
──────────────────────────────────────────────────────────────────────────
* doc/roadmap/phases.md — Phase 9a split into 9a.1 + 9a.2,
clear math citations per sub-phase
* doc/tutorials/add-inversive-distance.md — corrects the prior claim
that InversiveDistanceFunctional.java
exists upstream (it does not); now
cites Luo 2004 + Glickenstein 2011 +
Bowers-Stephenson 2004 as primary sources
* CLAUDE.md — adds phase-9a-validation.md to doc map
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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