Simplified codebase #27
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stemangiola
commented
Oct 25, 2025
stemangiola
commented
- Removed design parameter from print.SummarizedExperiment function
- Updated print method to streamline functionality
- Adjusted documentation to reflect changes in print method
- Updated RoxygenNote to 7.3.3
- Added import for dplyr's all_of function in NAMESPACE
- Removed design parameter from print.SummarizedExperiment function - Updated print method to streamline functionality - Adjusted documentation to reflect changes in print method - Updated RoxygenNote to 7.3.3 - Added import for dplyr's all_of function in NAMESPACE
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Pull Request Overview
This PR simplifies the print.SummarizedExperiment function by removing the design parameter and consolidating the print method to use only the "tidyprint_1" style. The changes streamline the codebase by eliminating multiple print design options (SummarizedExperiment, tidySummarizedExperiment, plyxp, and tidyprint_1) in favor of a single consistent output format.
Key changes:
- Removed the
designparameter fromprint.SummarizedExperiment, defaulting to the tidyprint_1 style - Deleted ~180 lines of code related to alternative print designs
- Updated documentation to reflect the simplified API
Reviewed Changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| R/print_methods.R | Removed design parameter and consolidated to single print style, added all_of import |
| man/print.SummarizedExperiment.Rd | Updated documentation to remove design parameter references |
| tests/testthat/test-print_methods.R | Removed tests for deprecated design parameter options |
| NAMESPACE | Added import for dplyr's all_of function |
| DESCRIPTION | Bumped version to 0.99.6 and updated RoxygenNote to 7.3.3 |
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R/print_methods.R
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| print_tidyprint_1 <- function(x, n = n_print , ...){ | ||
| # SE_print_abstraction | ||
| print_tidyprint_1 <- function(x, n = n_print , ...){ |
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Extra space before closing parenthesis in function parameter list. Remove the space before the comma for consistency: n = n_print, ...)
Suggested change
| print_tidyprint_1 <- function(x, n = n_print , ...){ | |
| print_tidyprint_1 <- function(x, n = n_print, ...){ |
- Changed parameter name in print.SummarizedExperiment function for clarity - Updated documentation and examples to reflect the new parameter name - Adjusted internal logic to use the new parameter name consistently - Updated tests to verify functionality with the new parameter name
Update print method parameter from n_print to n
- Updated internal logic to replace n_print with n for improved clarity and consistency - Adjusted row and column slicing logic to accommodate the new parameter - Enhanced separator row handling for better output formatting - Maintained attribute management for the output tibble
Refactor print.SummarizedExperiment function
…nd clarify display features for SummarizedExperiment objects. Removed deprecated visualizations and streamlined content for better accessibility and user experience.
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