Deprecate threads argument across dig_* functions

[Copilot]

This PR aligns threads handling with the existing lifecycle-based deprecation pattern used for deprecated arguments in dig_associations(). The threads argument is now consistently deprecated across all dig_* APIs that expose it.

• API deprecation alignment

  • Updated these exported functions to use threads = deprecated():
    • dig_associations()
    • dig_grid()
    • dig_correlations()
    • dig_baseline_contrasts()
    • dig_complement_contrasts()
    • dig_paired_baseline_contrasts()
    • dig_tautologies()

• Lifecycle warning behavior

  • Added lifecycle::is_present(threads) checks with deprecate_warn(...) in each affected function.
  • Kept backward-compatible behavior by defaulting to threads <- 1L when threads is omitted in core call paths.

• Nested call de-duplication

  • Internal forwarding paths now pass a deprecate_threads = FALSE flag in error_context where needed to avoid repeated warnings when one deprecated public API calls another.

• Documentation updates

  • Updated @param threads roxygen text in all affected files to explicitly mark the argument as deprecated.

dig_correlations <- function(..., threads = deprecated()) {
    if (lifecycle::is_present(threads)) {
        deprecate_warn(
            when = "2.2.0",
            what = "nuggets::dig_correlations(threads)",
            details = "The `threads` argument is deprecated and will be removed in future versions."
        )
    }
    ...
}

[beerda]

@copilot change the "when" version to "2.3.0"

[Copilot]

@copilot change the "when" version to "2.3.0"

Updated to when = "2.3.0" in the affected deprecation warnings. Fixed in commit 548a2b6.

[beerda]

@copilot you have wrongly updated the "when" value also in other cases than just for threads argument. Fix it = revert the "when" value for occurences other than for "threads". Also put the deprecation test of "threads" argument just before ".must_be...." test of threads.

[codecov]

Codecov Report

❌ Patch coverage is 46.34146% with 22 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.13%. Comparing base (a2b5a85) to head (ced07ae).

Files with missing lines	Patch %	Lines
R/dig_associations.R	50.00%	4 Missing ⚠️
R/dig_baseline_contrasts.R	40.00%	3 Missing ⚠️
R/dig_complement_contrasts.R	40.00%	3 Missing ⚠️
R/dig_correlations.R	40.00%	3 Missing ⚠️
R/dig_grid.R	57.14%	3 Missing ⚠️
R/dig_paired_baseline_contrasts.R	40.00%	3 Missing ⚠️
R/dig_tautologies.R	50.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel      #53      +/-   ##
==========================================
+ Coverage   87.09%   87.13%   +0.04%     
==========================================
  Files         127      127              
  Lines        6469     6508      +39     
==========================================
+ Hits         5634     5671      +37     
- Misses        835      837       +2     

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[Copilot]

@copilot you have wrongly updated the "when" value also in other cases than just for threads argument. Fix it = revert the "when" value for occurences other than for "threads". Also put the deprecatio...

Fixed. I reverted when back to "2.2.0" for non-threads deprecations and moved threads deprecation checks to just before the downstream threads validation path. Commit: 3523350.

[beerda]

@copilot deprecate "threads" also in "dig()" function in R/dig.R

[Copilot]

@copilot deprecate "threads" also in "dig()" function in R/dig.R

Implemented in dig() in /home/runner/work/nuggets/nuggets/R/dig.R with lifecycle deprecation warning and omitted-value fallback. Also suppressed duplicate nested warning in dig_grid() forwarding. Commit: 0ff93b6.

[beerda]

@copilot fix duplicate nested warning also in other dig* functions after you have introduced that warning in dig()

[Copilot]

@copilot fix duplicate nested warning also in other dig* functions after you have introduced that warning in dig()

Checked and aligned all nested dig* call chains for threads deprecation suppression: callers forward deprecate_threads = FALSE to avoid duplicate warnings (dig_tautologies -> dig_associations, dig_correlations/dig_*_contrasts -> dig_grid, and dig_grid -> dig). The dig_grid -> dig part was added in commit 0ff93b6; wrapper suppressions are already in place.