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[smasongarrison]

Pull Request Template

Description

Update to 1.4.1 in prep for cran update

[Copilot]

Pull Request Overview

This pull request updates the package to version 1.4.1 in preparation for a CRAN update. The key changes include replacing all print calls with message for verbose output, updating the mapping key from spID to spouseID in the internal standardization function, and updating documentation as well as metadata (NEWS, NAMESPACE, and DESCRIPTION).

Reviewed Changes

Copilot reviewed 25 out of 25 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
man/standardizeColnames.Rd	Removed the internal keyword from the Rd file.
man/simulatePedigree.Rd	Changed verbose print calls to message.
man/buildBetweenGenerations.Rd	Changed verbose print calls to message.
R/tweakPedigree.R	Replaced commented-out print calls with message calls.
R/simulatePedigree.R	Updated all verbose output from print to message.
R/readWikifamilytree.R, etc.	Similar verbose output changes with print replaced by message.
R/cleanPedigree.R	Updated the mapping key from "spID" to "spouseID".
NEWS.md, NAMESPACE, DESCRIPTION	Package metadata updated to reflect version 1.4.1 and new exports.

Comments suppressed due to low confidence (1)

R/cleanPedigree.R:22

• The mapping key was updated from 'spID' to 'spouseID'. Please verify that all downstream references and documentation are updated accordingly.

"spouseID" = "^(?:s(?:pt?)?id|spouse[\.\-_]?(?:id)?|partner[\.\-_]?(?:id)?|husb(?:and)?[\.\-_]?id|wife[\.\-_]?(?:id)?|pid[\.\-_]?spouse1?)",

[codecov]

Codecov Report

Attention: Patch coverage is 82.41758% with 16 lines in your changes missing coverage. Please review.

Project coverage is 84.59%. Comparing base (104ca90) to head (7554e8f).
Report is 25 commits behind head on main.

Files with missing lines	Patch %	Lines
R/checkParents.R	66.66%	9 Missing ⚠️
R/readGedcom.R	62.50%	3 Missing ⚠️
R/readWikifamilytree.R	0.00%	2 Missing ⚠️
R/readGedcomlegacy.R	88.88%	1 Missing ⚠️
R/simulatePedigree.R	94.44%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #69      +/-   ##
==========================================
+ Coverage   83.60%   84.59%   +0.98%     
==========================================
  Files          23       23              
  Lines        3435     3448      +13     
==========================================
+ Hits         2872     2917      +45     
+ Misses        563      531      -32     

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[Copilot]

Pull Request Overview

This PR updates the package to version 1.4.1 in preparation for a CRAN update. Key changes include replacing print() calls with message() for verbose output, renaming identifier fields (e.g. "id" to "personID") for consistency, and adding new aliases for the "mitochondrial" component in various functions.

Reviewed Changes

Copilot reviewed 66 out of 66 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
R/readWikifamilytree.R	Replaces print with message for verbose file reading.
R/readGedcomlegacy.R	Updates messaging and variable naming for consistency.
R/readGedcom.R	Renames the identifier field from "id" to "personID".
R/plotPedigree.R	Uses message instead of print for verbose output.
R/insertEven.R	Replaces print with message for improved logging.
R/helpPedigree.R, R/helpGeneric.R	Minor messaging updates in help functions.
R/constructAdjacency.R, R/buildComponent.R	Adds extra aliases for "mitochondrial" handling.
R/checkSex.R, R/checkPedigreeNetwork.R, R/checkParents.R, R/checkIDs.R	Updates messaging for validations and repairs.
R/calculateFamilySize.R	Updates logging from print to message.
R/cleanPedigree.R	Updates regex mapping for standardized column names.
NEWS.md, NAMESPACE, DESCRIPTION, BGmisc_main.code-workspace, .github/workflows/R-CMD-dev_maincheck.yaml	Documents version and dependency changes, workspace, and CI updates.

Comments suppressed due to low confidence (1)

R/readGedcom.R:187

• Ensure consistent use of 'personID' throughout the function and update any associated documentation to reflect the renaming from 'id'.

record$personID <- stringr::str_extract(line, "(?<=@.)\d*(?=@)")

[Copilot]

Consider creating a robust template row for new parent entries rather than indexing the first row of an empty dataframe to ensure the template always has the correct structure.

Suggested change

	new_entry_base <- new_entries[1, ]
	new_entry_base <- as.data.frame(lapply(ped_columns, function(col) {
	if (is.numeric(ped[[col]])) NA else if (is.character(ped[[col]])) NA_character_ else NA
	}))
	colnames(new_entry_base) <- ped_columns