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- CI: bump julia-actions/setup-julia to v2, codecov-action to v5 with CODECOV_TOKEN; switch matrix to 'min' + '1'. - TagBot: use TAGBOT_TOKEN; register against HolyLab/HolyLabRegistry. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Targets the upcoming v1 releases of CachedInterpolations, CenterIndexedArrays, RegisterCore, RegisterDeformation, RegisterFit, and RegisterPenalty. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- TimeHessian `*` and `mul!`: swap to `penalty!(g, ϕs, λt)` to match the new argument order of the time-only `penalty!` overload in RegisterPenalty v1. - Test "Optimization with a temporal penalty": call the 3-arg `quadratic` as `quadratic(denom, shift, Q)`, matching the new RegisterUtilities v1 signature that takes the denominator first. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Preflight baseline established (CHUNK-001 complete): 200/200 tests pass, 0 ambiguities at 7f64c5a. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Removes `initial_deformation(ap, cs, Qs, ϕ_old, maxshift)` (body was
`error("This is broken, don't use it")`) and `optimize(::AffineMap,
mmis, nodes)` (used a pre-MathProgBase Optim API that no longer
exists). Also removes all support code reachable only from those two
methods: `InitialDefOpt`, the 4-arg `find_opt` overload, the
`MOI.eval_objective`/`eval_objective_gradient`/`_eval_f` trio for
`InitialDefOpt`, both `affine_part!` methods on `Φ<:GridDeformation`,
and the `optimize`-only helpers `affinepenalty!` and `_calculate_u`.
Trims the surviving `initial_deformation` docstring to drop the now-
misleading `[ϕ_old=identity]` keyword.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
`auto_λ(stackidx::Integer, cs, Qs, nodes, mmis, λrange)` put a configuration integer before data — wrong order by Julia convention. Fold it into `auto_λ(cs, Qs, nodes, mmis, λrange; stackidx=nothing)` and slice inside the body when set. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
optimize_rigid (rigid-search cluster, CHUNK-004): - Move SD and maxrot from positional to keyword arguments; SD defaults to identity of size ndims(fixed) computed lazily in the body. - Rename tol → atol (consistent with Base.isapprox / IterativeSolvers). - Forward extra kwargs to Ipopt via optimizer_with_attributes so callers can set any Ipopt option without a new overload. rotation_gridsearch (rigid-search cluster, CHUNK-005): - Move SD from positional to keyword; same lazy default as above. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
initial_deformation: fold the 4-arg positional-λt overload (Method 4)
into the SVector-typed Method 2 via a λt=nothing keyword; both paths
now live in one function body. The bare Method 1 gains λt=nothing
for forward-compat.
optimize!(::Vector{<:GridDeformation}, …): move λt from position 4 to
keyword. Add a Vector{<:GridDeformation} type constraint on the first
argument to prevent AffinePenalty specificity from stealing single-
frame dispatch. λt=nothing maps to zero(T).
fixed_λ: merge the SVector-typed temporal overload and its flat-array
adapter into the generic method (λt=nothing keyword; temporal branch
when λt≠nothing) and the unified flat-array adapter.
Update test call sites and docstrings throughout.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
CHUNK-007: Remove auto_λt(Es, cs::Array{Tf}, Qs::Array{Tf}, ap, λt) —
a flat-array adapter misleadingly named (λt was actually λtrange).
Consistent with similar adapters removed from auto_λ, fixed_λ, and
optimize! in this review. Callers must now pass SVector/SMatrix-typed
cs/Qs directly.
CHUNK-008: Relax auto_λ flat-array overloads:
- T3-C: independent element types — replace the shared-Tf constraint
(cs::Array{Tf}, Qs::Array{Tf}, mmis::Array{Tf}) with independent
AbstractArray{<:Number} annotations.
- T2-C: widen Array{Float64} to AbstractArray{Float64}; collect to a
dense Array inside the body before reinterpret/reshape.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
First stable release. All breaking API changes from the API review are included in this version; see CHANGELOG.md for the full list. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #41 +/- ##
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+ Coverage 33.48% 36.25% +2.76%
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Files 1 1
Lines 642 571 -71
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- Hits 215 207 -8
+ Misses 427 364 -63 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Summary
initial_deformation(ap, cs, Qs, ϕ_old, maxshift)(body waserror("This is broken")) andoptimize(::AffineMap, mmis, nodes)(used a pre-MathProgBase Optim API)stackidxonauto_λ;SD/maxrotonoptimize_rigid;SDonrotation_gridsearch;λtoninitial_deformation,optimize!, andfixed_λtol→atolonoptimize_rigid(consistent withBase.isapprox); addkwargs...passthrough to Ipoptauto_λtflat-array adapter overload (misleadingly named; same pattern as adapters removed elsewhere)auto_λflat-array overloads fromArray{Tf}(shared element type) to independentAbstractArray{<:Number>Also includes prep commits that landed before the baseline: CI/TagBot modernization, compat bumps for the Register* family to v1, and two-line adaptations for the RegisterPenalty/RegisterUtilities v1 API changes.
Test plan
Test.detect_ambiguities(RegisterOptimize)= 0 throughout@JuliaRegistrator register🤖 Generated with Claude Code