Creating a default print for sr_model

[sschildhauer]

Three CI failures in the print.sr_model PR: tidyselect deprecation warnings from .data in non-data-masking contexts, Rd files out of sync with source, and a missing snapshot for the unstratified test case.

Changes

• Fix .data in tidyselect contexts — .by, names_from, and values_from are tidyselect args, not data-masking; replaced with string column names:

  # Before
  dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, .data$Parameter), ...)
  tidyr::pivot_wider(names_from = .data$Parameter, values_from = .data$median_val)
  
  # After
  dplyr::summarise(.by = c("Stratification", "Iso_type", "Parameter"), ...)
  tidyr::pivot_wider(names_from = "Parameter", values_from = "median_val")

• Regenerate documentation — ran devtools::document() to sync man/print.sr_model.Rd and four other Rd files that had drifted from source; also fixed [dplyr::tbl_df] → [tibble::tbl_df] in the print_tbl param doc.

• Add missing snapshot — added the Linux/non-Darwin snapshot for the unstratified sr_model print test (the macOS variant will be generated by CI on the first passing run).

[codecov]

Codecov Report

❌ Patch coverage is 94.73684% with 1 line in your changes missing coverage. Please review.
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
R/print.sr_model.R	94.73%	1 Missing ⚠️

Files with missing lines	Coverage Δ
R/Run_Mod.R	100.00% <ø> (ø)
R/expect_snapshot_data.R	100.00% <ø> (ø)
R/print.sr_model.R	94.73% <94.73%> (ø)

[github-actions]

📖 https://ucd-serg.github.io/serodynamics/preview/pr114
Preview documentation for this PR (at commit 7888183)

[sschildhauer]

I am a little confused with the warning/error I am getting here. It looks like there is a scoping issue relating to the base dataset when using dplyr, but when I fix the issue the tests are producing a warning. It seems like the solution might be in conflicting with each other. Grateful for any help!

[sschildhauer]

@copilot apply changes based on the comments in this thread

[Copilot]

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated 4 comments.

[Copilot]

@copilot apply changes based on the comments in this thread

Applied in commit 6384e0c:

• Removed suppressWarnings() from around pivot_wider() entirely — confirmed it produces no warnings when called on properly summarised data (each Parameter value appears exactly once per Stratification/Iso_type combination). The original warnings being suppressed were the tidyselect .data deprecation warnings, which were already fixed in a prior commit.
• Updated the snapshot for the "no strat" test to match the test code that now calls print(results, print_tbl = TRUE).

The pipeline in print.sr_model() is now a clean chain with no warning suppression needed.

[Copilot]

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated 5 comments.

[sschildhauer]

@copilot apply changes based on the comments in this thread

[Copilot]

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