refactor: convert magrittr %>% to base |> and ensure RHS calls use pa…#159

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stemangiola wants to merge 18 commits intomasterfrom

chore/convert-to-base-pipe

Commits on Oct 25, 2025

refactor: convert magrittr %>% to base |> and ensure RHS calls use parentheses; fix subset and validation piping edge cases; replace placeholder _ indexing; update tests and vignettes
stemangiola
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fix the pipe conversion
stemangiola
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Convert magrittr pipes to base R pipes
stemangiola
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Fix annotation_group examples to prevent CI/CD failures
stemangiola
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Fix discarded pipe result in utilities.R
stemangiola
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Refactor color mapping and data filtering logic

cursoragent
and
stemangiola
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Fix remaining when() calls and break pipe chains with if statements
stemangiola
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Fix all remaining when() calls and break pipe chains
stemangiola
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Use case_when() for cleaner conditional logic
stemangiola
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Fix as_matrix function to work with base R pipes
stemangiola
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Fix validation function parameter names for base R pipes
stemangiola
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Fix logical condition in subset function for column validation
stemangiola
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Fix %in% operator precedence issues with base R pipes
stemangiola
committed