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Depend on juliabridge, which juliaready was renamed to - #44
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Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk>
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WalkthroughChangesJuliabridge migration
Suggested reviewers: Priority: ➖ Normal Change: Feature Merge Risk: 🟡 Moderate · up to
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marked this pull request as ready for review
October 12, 2026 21:06
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approved these changes
Oct 14, 2026
* Build model specifications with juliabridge Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk> * Simulate from any model specification, whatever role it carries Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk> * Give DiffLatentModel one initial value per difference Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk> * Read the infection model only where there is one to read Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk> * Ask whether the Julia session is still there before forecasting Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk> * Leave an init slot that is already whole as it was written Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk> * Leave matching Julia to the Manifest to juliabridge Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk> * Test the probe composableIDModelR supplies, not juliabridge's answer Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk> --------- Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk>
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Actionable comments posted: 2
- 🪄 Fix comments: Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at @DESCRIPTION:
- Line 21: Update the juliabridge dependency in DESCRIPTION to require version
0.1.0 or later and pin its remote to the compatible v0.1.0 tag. Add a package
load-time check in the .onLoad flow near .role_labels that rejects juliabridge
unless its exported assert_role function has a labels argument.
Review comments at @tests/testthat/test-julia.R:
- Line 74: Update the stale-session error assertion in the test around
`predict(stale, horizon = 2)` to expect “has gone”, matching the error returned
by `predict.cidm_fit()` and the new setup test.
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📒 Files selected for processing: 53
DESCRIPTIONNAMESPACENEWS.mdR/dist-convert.RR/distributions.RR/fit.RR/id-model.RR/infection-models.RR/julia-code.RR/julia-spec.RR/latent-models.RR/methods.RR/observation-models.RR/setup.RREADME.RmdREADME.mdman/IDModel.Rdman/as_julia.Rdman/as_julia_value.dist_spec.Rdman/cidm_available.Rdman/component.Rdman/distributions.Rdman/dot-as_prior.Rdman/dot-assert_role.Rdman/dot-format_code.Rdman/dot-join_lines.Rdman/dot-julia_handle.Rdman/dot-juliaup_julia.Rdman/dot-manifest_julia_version.Rdman/dot-render.Rdman/dot-render_call.Rdman/dot-render_float.Rdman/dot-render_kwargs.Rdman/dot-render_string.Rdman/dot-render_vector.Rdman/fit.Rdman/infection-models.Rdman/julia.Rdman/latent-models.Rdman/nuts.Rdman/observation-models.Rdman/plot.cidm_fit.Rdman/predict.cidm_fit.Rdman/reexports.Rdman/simulate.julia_spec.Rdman/summary.cidm_fit.Rdtests/testthat/test-components.Rtests/testthat/test-fit.Rtests/testthat/test-julia-code.Rtests/testthat/test-julia-spec.Rtests/testthat/test-julia.Rtests/testthat/test-setup.Rvignettes/composableIDModelR.Rmd
💤 Files with no reviewable changes: 16
- man/dot-manifest_julia_version.Rd
- man/dot-render.Rd
- man/dot-join_lines.Rd
- man/dot-format_code.Rd
- man/dot-render_string.Rd
- tests/testthat/test-julia-code.R
- man/dot-render_vector.Rd
- man/dot-render_float.Rd
- man/dot-render_kwargs.Rd
- man/dot-juliaup_julia.Rd
- man/component.Rd
- man/dot-render_call.Rd
- man/as_julia.Rd
- man/julia.Rd
- man/dot-julia_handle.Rd
- R/julia-code.R
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Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk>
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The scheduled
R-CMD-checkhas been red since 5 October.Remotes: sbfnk/juliareadyno longer resolves: the repository moved toepiforecasts/juliabridge, and the package inside it was renamed too. pakgives up before installing anything. Only the weekly run caught it; the last
push-triggered check predates the rename.
This updates the
ImportsandRemotesentries, the fourjuliaready::callsites in
R/setup.R, and the.packageargument of a mocked binding in thesetup tests. The setup tests pass.
Summary by CodeRabbit
julia_spec()for constructing Julia model components, with role-aware specifications and support for Julia code and value conversion.Rtfor models that do not support it.