Bootstrap CI workflows and update DESCRIPTION#23
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Sets up the GitHub Actions CI baseline for the CRAN push: - R-CMD-check.yaml: 3-OS x 3-R-version matrix (ubuntu/macos/windows release/oldrel/devel) with --as-cran, Stan compile cache, devel jobs continue-on-error. Adapted from the imuGAP / imugap-map CI pattern. - lint.yaml: lintr on every push/PR with LINTR_ERROR_ON_LINT=true. Expected to fail on main until the lint cleanup PR lands; surfacing the violations is the point. - test-coverage.yaml: covr::package_coverage on ubuntu-release, cobertura.xml uploaded as artifact. (Codecov hookup deferred until a CODECOV_TOKEN secret is configured.) - .Rbuildignore: exclude .github/ from the built package. - DESCRIPTION: replace roxygen2 boilerplate with real Title, Description, and Authors@R (Claire P. Smith as cre/aut, Jack Goodall as aut, based on git history). Wording is a starting point — please refine on review. Closes #9, #10.
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May 22, 2026 15:19
R-CMD-check on the initial CI run surfaced two issues that block check across all platforms: - Tests fail with "there is no package called 'dplyr'" because the package uses dplyr/Claddis/posterior/stringr/tidyr via :: but none of those are declared in Imports. Add them. - ERROR: configure exists but is not executable. Set the executable bit on configure (the standard rstantools-generated stub that runs rstan_config() at install time). Refs #9, #10.
macOS jobs failed building 'expm' (a transitive dep) from source: fatal error: 'libintl.h' file not found macOS doesn't ship GNU gettext headers; libintl.h has to come from brew. Add the same brew + ~/.R/Makevars setup imuGAP uses to expose the gettext include + lib paths to R's source-package compilation. Refs #9.
This was referenced May 22, 2026
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@csmith701 — this is the first PR in the CRAN push tracked in #22. Ready for your review. A few things worth flagging: DESCRIPTION is a starting point, not a final draft:
Two CI failures are intentional, please don't be alarmed:
Two real bugs this PR surfaced and fixed:
What's next (per #22):
No rush — flag anything that needs changing. |
This was referenced May 22, 2026
pearsonca
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May 27, 2026
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Claire will need to fix the package title, otherwise looks good for basic sketch out.
we should have a look at trimming down dependency list
| @@ -1,24 +1,37 @@ | |||
| Package: hestia | |||
| Title: What the Package Does (One Line, Title Case) | |||
| Title: Bayesian Compartmental Infection Models from Individual Outcomes | |||
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@csmith701 Household ESTimation for Infection Analysis? I forget precisely what hestia stands for, but roughly that.
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@csmith701 friendly ping, this one's just waiting on you. Per @pearsonca's review the only blocker is the package title in Separately, I split Carl's dependency-trimming note into #33 so it doesn't hold up this PR. |
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Summary
First PR in the Week-5 plan from #22 — sets up GitHub Actions CI and replaces the roxygen2 boilerplate in DESCRIPTION. Bundled per the tracking issue's plan because CI needs a valid DESCRIPTION to run R CMD check at all.
Changes
.github/workflows/R-CMD-check.yaml— 3-OS × 3-R-version matrix (ubuntu/macos/windows×release/oldrel/devel) running--as-cran. Stan compile artifacts cached per OS+R version. R-devel jobs arecontinue-on-error: trueto absorb upstream churn (Bioconductor / R-devel breakage). Adapted from the imuGAP / imugap-map CI pattern..github/workflows/lint.yaml—lintr::lint_package()on every push/PR,LINTR_ERROR_ON_LINT: true. Expected to fail on main until the lint cleanup PR (Linting #8) lands; surfacing the violations is the entire point..github/workflows/test-coverage.yaml—covr::package_coverage()on ubuntu-release, uploadscobertura.xmlas an artifact. Codecov upload step deferred until aCODECOV_TOKENrepo secret is configured..Rbuildignore— exclude.github/so workflow files don't end up in the built source tarball.DESCRIPTION— replaces roxygen2 boilerplate:Title:Bayesian Compartmental Infection Models from Individual OutcomesDescription:first-pass wording, see belowAuthors@R:Claire P. Smith (cre/aut, ORCID from imuGAP record) and Jack Goodall (aut), based on git history.Open questions for review
cresince she's the primary code author per git log. Carl is not currently listed; add if appropriate. Jack Goodall isaut; downgrade toctbif that's more accurate. Emails are pulled from git log.CODECOV_TOKENis set (mirrors imuGAP #46).What CI will look like on this PR
Expect:
R-CMD-checkmatrix — probably green on linux/mac, may surface DESCRIPTION-related notes or Stan-on-Windows issues we haven't seen before.lint— will fail. That's expected; PR 2 (Linting #8) cleans up.test-coverage— should pass on ubuntu-release.Opened as draft so we can iterate based on actual CI output.
Closes #9, #10.
Refs #22.