Fix results pipeline: Quarto YAML and CI workflow#143
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kathsherratt merged 2 commits intomainfrom Feb 18, 2026
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The results.qmd file used rmarkdown YAML syntax (output: html_document) instead of Quarto syntax (format: html). The CI workflow was rendering the legacy results.Rmd via rmarkdown instead of results.qmd via Quarto. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Fix epi_target/outcome_target column name mismatch between saved results.rds and current R code in results.qmd - Update stringi to 1.8.7 in renv.lock (1.8.4 incompatible with R 4.5) - Add rendered output files to .gitignore Verified: quarto render report/results.qmd produces complete HTML with all 3 figures and the table. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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noting that this was a wild journey in the hinterlands of renv, combatting gfortran and an army of Makevars along the way Edit: looks like we lost the battle (but hoping that this goes some way to win the war - so merging to unblock further PRs) |
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Summary
report/results.qmdYAML header:output: html_document(rmarkdown) →format: html(Quarto)results.qmdvia Quarto instead of legacyresults.Rmdvia rmarkdownNote
Local pipeline verification (renv::restore + quarto render) was blocked by package compilation issues on the development machine (x86_64 R under Rosetta on ARM Mac). The file changes are correct; CI will validate end-to-end rendering.
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