Modernize package for CRAN v1.0.3#13
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- Add testthat (edition 3) suite covering every exported function and bundled dataset; no code changes to exports. - Expand R-CMD-check workflow to a macOS/Windows/Ubuntu matrix across R-release, R-devel and R-oldrel-1. - Add test-coverage workflow (covr + Codecov) and pkgdown workflow that deploys https://ald0405.github.io/SangerTools/ on push to master. - Add new demo-data-and-functions vignette walking through all bundled datasets and every exported function in one notebook. - Document that df_to_sql() targets SQL Server via ODBC under Windows integrated security (behaviour unchanged). - Refresh README badges: drop dead AppVeyor, add R-CMD-check, codecov, pkgdown, lifecycle. - Bump declared minimum R version from 2.10 to 3.5.0 and RoxygenNote to 7.3.2. - Add URL, BugReports, _pkgdown.yml, codecov.yml, .lintr. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
master_patient_index$Age is stored as double in the bundled .rda; only check is.numeric() rather than expect_type "integer". Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Add render-notebook workflow that knits vignettes/demo-data-and-functions.Rmd into notebooks/demo-data-and-functions.md (GitHub-flavoured Markdown, with embedded figures) and commits the rendered output back to the same branch on every push that touches the vignette. README now links to the rendered notebook so reviewers can browse it directly on github.com. notebooks/ is in .Rbuildignore so the rendered output does not ship in the CRAN tarball. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Bring SangerTools out of its 2022-era state into a CI-verifiable, modern CRAN-ready shape. No exported API changes — same functions, same arguments, same bundled datasets.
testthat(edition 3) suite covering every exported function and bundled dataset (previously: zero tests).R-CMD-check.yamlexpanded to a{macOS, Windows, Ubuntu} x {R-release, R-devel, R-oldrel-1}matrix usingr-lib/actions/*@v2. Newtest-coverage.yaml(covr + Codecov) andpkgdown.yaml(deploys togh-pages).vignettes/demo-data-and-functions.Rmdwalks through all three bundled datasets and exercises every exported function in one notebook. pkgdown reference grouped into Analytics / Wrangling / Charts / I/O / Datasets via_pkgdown.yml.df_to_sql(): added@detailsblock clarifying that the function targets Microsoft SQL Server via ODBC under Windows integrated security. No code change.DESCRIPTIONbumped toVersion: 1.0.3,Depends: R (>= 3.5.0)(was2.10),RoxygenNote: 7.3.2, addedURL/BugReports, addedpkgdownandcovrtoSuggests.cran-comments.md: refreshed with the new CI matrix; final numbers to be filled in once this PR is green..Rbuildignoreupdated;.lintrandcodecov.ymladded;README.mdremoved from.gitignore(it was incorrectly ignored).Test plan
CI does the verification — that's the whole point of this PR.
R-CMD-checkmatrix all green (5 jobs).test-coverageworkflow uploads to Codecov successfully.pkgdownworkflow builds and (on merge to master) deploys to https://ald0405.github.io/SangerTools/.cran-comments.mdand fill in the matrix result line once green.rhub::rhub_check()cloud run to cover CRAN flavours not in the GitHub matrix (Fedora-clang, Debian-clang) before submitting.devtools::release()ordevtools::submit_cran()manually — CRAN requires a human form upload.🤖 Generated with Claude Code