feat: covariate-requirement introspection (#266)#293
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Adds required_covariates(tree), listing the covariate names a tree's Varying leaves and data-selected Choose disjunctions will read, keyed to the node paths that read them; required_parameters(tree), the symmetric sibling over unpinned (estimated) parameters read off params_table; and missing_covariates(tree, ctx), checking a Context against the former so a caller can validate a data source's columns up front instead of discovering a gap reactively, one covariate at a time, mid-instantiate. Lives in varying.jl alongside the existing has_varying guard (introspection.jl loads before Varying/Shared/Choose exist, so the walk needs their types already defined). Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
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Try this Pull Request!Option 1: Julia Package ManagerOpen Julia and type: import Pkg
Pkg.activate(temp=true)
Pkg.add(url="https://github.com/EpiAware/ComposedDistributions.jl", rev="feat/covariate-requirements-266")
using ComposedDistributionsOption 2: Local CheckoutIf you have the repo locally: git checkout feat/covariate-requirements-266
julia --project=. -e "using Pkg; Pkg.instantiate()" |
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Benchmark comparison vs baseMinimum time per call. Buckets are PR time as a % of base, so lower is faster (🟢 faster, ⚪ within 5%, 🔴 slower). Counts of benchmarks per bucket:
Evaluation — 17 benchmarks (by time change)
AD gradients — 28 benchmarks (by time change)
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Summary
required_covariates(tree)lists the covariate names a tree'sVaryingleaves and data-selectedChoosedisjunctionswill read, keyed to the node paths that read them (
Dict{Symbol, Vector{Symbol}}), so a caller can validate a data source's columns upfront instead of discovering a gap reactively, one covariate at a time,
mid-
instantiate.required_parameters(tree)is the symmetric sibling: the unpinned(estimated) parameters a tree's
params_tablestill needs, as(edge, param)pairs (every row whoseprioris notnothing).missing_covariates(tree, ctx)checks aContextagainstrequired_covariates, returning the (possibly empty) vector of names thecontext is missing, reporting every gap at once rather than the first one
instantiatehappens to reach.Choose's ownselectorrequirement is labelled with a:selectorsuffix (mirroring how
params_tablelabels aResolve's ownbranch_probsrow), so a root-levelChoosereports a real edge nameinstead of an empty path.
varying.jlalongside the existinghas_varyingguard:introspection.jlloads beforeVarying/Shared/Chooseexist, so thenew tree walk (which needs those types for its per-node dispatch) can't
live there without a forward-reference load error.
Closes #266.
Test plan
@testitem "required_covariates / required_parameters / missing_covariates (#266)": a stationary tree (empty), a singleVaryingleaf, two leaves sharing one covariate name, aVaryingnested inside a
Resolveoutcome, a root-level and nestedChooseselector requirement (plus a
Choosealternative that itselfcontains a
Varyingleaf), and anuncertainleaf's estimatedparameter.
task test-fast— 1543/1543 passed.This was opened by a bot. Please ping @seabbs for any questions.