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Merged
d-morrison merged 6 commits into from
Jan 21, 2026
Merged

Merge main branch and fix workflow failures #486

d-morrison merged 6 commits into from
Jan 21, 2026

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Copilot AI commented Jan 20, 2026 •
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Thank you for taking the time to submit a pull request!

To maximize the chances of acceptance:

  • The title of your PR should briefly describe the change.
  • Commit/merge messages to be included in NEWS.md should begin with -.
  • Code should follow the tidyverse style guide.
  • Documentation should use roxygen2, with Markdown syntax.
  • Contributions should include unit tests (using testthat).

For more information see Contributing.

Changes

Merged latest main branch into decay-curve-2 feature branch to incorporate upstream changes and fixed all resulting workflow failures.

Conflicts Resolved

  • DESCRIPTION: Combined imports from both branches, removed duplicate mixtools (kept only in Suggests), removed unused pkgload, added missing config dependency
  • NAMESPACE: Combined exports from both branches (analyze_sims, antibody_decay_curve, compare_seroincidence, count_strata, curve_app, t1f, y1f) and imports (theme_bw, vars)
  • R/serocalculator-package.R: Retained both theme_bw and vars importFrom statements

Note: Used merge instead of rebase due to force-push restrictions.

Workflow Fixes

After merging, addressed all CI/CD workflow failures:

  • Linting Issues: Replaced stop() with cli::cli_abort() in R/autoplot.seroincidence.by.R and R/autoplot.seroincidence.R to comply with package style guidelines
  • Missing Shiny Imports: Added missing shiny function imports (h2, renderPlot, renderTable, sliderInput) for curve_app functionality
  • Data Masking Variables: Used .data pronoun in R/curve_app_server.R for proper data masking of variables (mu_y, mu_b, y0, b0, t1) within tibble construction, following tidyverse guidelines instead of utils::globalVariables() to eliminate R CMD check NOTEs
  • Partial Argument Matching: Fixed all sliderInput() calls in R/curve_app_ui.R by replacing abbreviated parameter val with the full parameter name value to eliminate R CMD check warnings

All tests pass and package loads successfully.

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

Copilot AI mentioned this pull request Jan 20, 2026
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@d-morrison
Merge main into decay-curve-2 branch and resolve conflicts
89d092b 
Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Copilot AI changed the title [WIP] Update decay curve implementation for analysis Merge main branch and resolve conflicts Jan 20, 2026
Copilot AI requested a review from d-morrison January 20, 2026 20:50
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codecov bot commented Jan 20, 2026 •
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Codecov Report

❌ Patch coverage is 79.66574% with 146 lines in your changes missing coverage. Please review.
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
R/sim_pop_data_multi.R 0.00% 29 Missing ⚠️
R/utils.R 23.52% 26 Missing ⚠️
R/graph_seroresponse_model_1.R 0.00% 21 Missing ⚠️
R/as_sr_params.R 20.00% 16 Missing ⚠️
R/strat_ests_scatterplot.R 70.00% 15 Missing ⚠️
R/curve_app_ui.R 0.00% 9 Missing ⚠️
R/curve_app_server.R 0.00% 8 Missing ⚠️
R/density_plot.R 90.74% 5 Missing ⚠️
R/load_sr_params.R 54.54% 5 Missing ⚠️
R/autoplot.seroincidence.R 25.00% 3 Missing ⚠️
... and 4 more
Files with missing lines Coverage Δ
R/ab1.R 100.00% <100.00%> (ø)
R/age_scatter.R 100.00% <100.00%> (ø)
R/analyze_sims.R 100.00% <100.00%> (ø)
R/autoplot.curve_params.R 100.00% <100.00%> (+100.00%) ⬆️
R/autoplot.pop_data.R 100.00% <ø> (+28.31%) ⬆️
R/autoplot.sim_results.R 100.00% <100.00%> (ø)
R/autoplot.summary.seroincidence.by.R 100.00% <100.00%> (ø)
R/check_parallel_cores.R 100.00% <100.00%> (ø)
R/check_pop_data.R 100.00% <100.00%> (ø)
R/check_strata.R 100.00% <100.00%> (ø)
... and 28 more

... and 6 files with indirect coverage changes

d-morrison
d-morrison requested changes Jan 20, 2026
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fix the code issues found by the failing workflows

@d-morrison
Fix workflow failures: linting and R CMD check issues
4e6b489 
Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
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Copilot AI commented Jan 20, 2026

fix the code issues found by the failing workflows

Fixed all workflow failures:

Linting issues: Replaced stop() with cli::cli_abort() in R/autoplot.seroincidence.by.R and R/autoplot.seroincidence.R

R CMD check issues:

  • Removed duplicate mixtools from Imports (kept in Suggests)
  • Removed unused pkgload from Imports
  • Added config to Imports (used in R/app_config.R)
  • Added missing shiny function imports (h2, renderPlot, renderTable, sliderInput)
  • Added utils::globalVariables declarations for curve_app variables (mu_y, mu_b, y0, b0, t1)

Package loads successfully and all tests pass. (commit 4e6b489)

Copilot AI changed the title Merge main branch and resolve conflicts Merge main branch and fix workflow failures Jan 20, 2026
Copilot AI requested a review from d-morrison January 20, 2026 22:59
d-morrison
d-morrison requested changes Jan 20, 2026
View reviewed changes
@d-morrison
Replace globalVariables with .data pronoun per tidyverse guidelines
151fbbf 
Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Copilot AI requested a review from d-morrison January 20, 2026 23:29
d-morrison
d-morrison requested changes Jan 21, 2026
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fix issues identified in latest workflow run (21191111690)

@d-morrison
Fix partial argument matching in sliderInput calls
b92fbfe 
Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
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Copilot AI commented Jan 21, 2026

fix issues identified in latest workflow run (21191111690)

Fixed partial argument matching issues in R/curve_app_ui.R - replaced all instances of val parameter with the correct value parameter in sliderInput() calls. This eliminates the R CMD check NOTEs about partial argument matching. (commit 0e30f17)

Copilot AI requested a review from d-morrison January 21, 2026 02:12
@d-morrison d-morrison marked this pull request as ready for review January 21, 2026 07:06
@d-morrison d-morrison merged commit 44cd17c into decay-curve-2 Jan 21, 2026
10 of 11 checks passed
@d-morrison d-morrison deleted the copilot/sub-pr-392 branch January 21, 2026 07:06
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