Develop #102

egenn · 2025-11-19T13:21:55Z

No description provided.

…` to `highlight`

…7 name representation functions.

gemini-code-assist · 2025-11-19T13:22:25Z

Summary of Changes

Hello @egenn, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on a significant refactoring effort to enhance and standardize the package's text formatting and object representation utilities. The primary goal is to improve code maintainability and consistency by renaming a key formatting function, introducing more flexible padding options, and streamlining how S7 object names are displayed. These changes ensure a more uniform and robust approach to console output and internal string manipulation.

Highlights

Function Renaming: The show_ls function has been renamed to repr_ls across the codebase, including its exports, usages in various S7 repr methods, and associated documentation and tests. This change aims to improve clarity and consistency in function naming.
Text Formatting Enhancements: The core fmt and highlight text formatting functions now support an additional pad parameter, allowing for more flexible control over text indentation and presentation. This enhancement has been propagated to relevant calls throughout the package.
Standardized Message Coloring: Direct usage of bold(green(...)) for status messages has been replaced with bold(highlight(...)) to standardize the visual representation of important information across various utility functions like print.CheckData, read, dt_merge, and ddb_data.
Refactoring of S7 Name Representation: The repr_S7name and objcat functions have been refactored to simplify their parameter list (e.g., colors replaced by col, verbosity removed, prefix added) and streamline the internal logic for generating S7 class name representations.
Removal of Unused Utilities: The leftpad and printchar utility functions, which were no longer needed due to changes in text formatting logic, have been removed from the codebase.

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gemini-code-assist

Code Review

This pull request appears to be a significant refactoring effort focused on improving code consistency and maintainability. Key changes include renaming show_ls to repr_ls throughout the project for better S7 compatibility, centralizing text formatting for colors and padding by enhancing the fmt function, and simplifying the repr_S7name function. These changes are applied consistently across code, documentation, and tests. The refactoring is well-executed, but I've identified one minor issue where a function argument is not being used as intended.

R/utils_strings.R

egenn · 2025-11-25T14:47:47Z

/gemini review

gemini-code-assist

Code Review

This pull request introduces several improvements and refactorings. The renaming of show_ls to repr_ls is a good change for clarity, though it is a breaking change for other packages in the ecosystem that might use this internal-but-exported function. The formatting functions have been enhanced, for example by adding a pad argument to fmt and highlight, which is a nice improvement. A new generic preprocessed has been added, which seems useful. I've found several instances where the new highlight function is redundantly wrapped in bold(). I've added comments with suggestions to remove the redundancy and in one case, to use the new pad argument for cleaner code.

R/14_S7_utils.R

R/read.R

Copilot

Pull request overview

This PR implements several refactoring improvements and API enhancements focused on code clarity, consistency, and maintainability. The changes include renaming functions for better naming conventions, removing unused code, standardizing styling functions, and adding new functionality for accessing preprocessed data.

Key changes:

Renamed show_ls() to repr_ls() to better reflect that it returns a string representation rather than printing
Replaced thin() with gray() and bold(green()) with highlight() for more semantic and consistent styling
Added new preprocessed() generic function to provide cleaner API access to preprocessed data from Preprocessor objects

Reviewed changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
DESCRIPTION	Updated package version to 0.99.1005 and date to 2025-11-25
NAMESPACE	Updated exports: removed `show_ls`, added `repr_ls` and `preprocessed`
R/00_S7_init.R	Added new `preprocessed()` generic function definition
R/01_S7_Hyperparameters.R	Updated function calls from `show_ls()` to `repr_ls()` and improved field documentation
R/02_S7_Metrics.R	Replaced `show_ls()` calls with `repr_ls()`
R/03_S7_Preprocessor.R	Added `preprocessed()` method for Preprocessor and updated `show_ls()` to `repr_ls()`
R/05_S7_Tuner.R	Updated `show_ls()` to `repr_ls()`
R/06_S7_Supervised.R	Clarified comment from "Refs & Res" to "References"
R/08_S7_ClusteringConfig.R	Replaced `show_ls()` with `repr_ls()`
R/09_S7_Clustering.R	Replaced `show_ls()` with `repr_ls()`
R/10_S7_DecompositionConfig.R	Updated `show_ls()` to `repr_ls()`
R/11_S7_Decomposition.R	Updated `show_ls()` to `repr_ls()`
R/14_S7_utils.R	Replaced `bold(green())` with `highlight()`
R/fmt.R	Added `pad` parameter to `fmt()` and `highlight()`, changed `gray()` to use explicit hex color, refactored to use intermediate variable
R/msg.R	Removed redundant `gray()` call in `msgdatetime()`
R/read.R	Replaced `bold(green())` with `highlight()` throughout
R/rtemis_color_system.R	Reordered variable assignments (no functional change)
R/utils_art.R	Replaced `thin()` with `gray()` for more semantic styling
R/utils_data.table.R	Replaced `bold(green())` with `highlight()` and `show_ls()` with `repr_ls()`
R/utils_duckdb.R	Replaced `bold(green())` with `highlight()`
R/utils_print.R	Renamed `show_ls()` to `repr_ls()`, removed unused `printchar()` function, replaced `thin()` with `gray()`
R/utils_strings.R	Updated function signature for `repr_S7name()` (replaced `colors`/`verbosity` with `col`/`prefix`), removed unused `leftpad()` function
man/fmt.Rd	Added `pad` parameter to documentation
man/highlight.Rd	Added `pad` parameter to documentation
man/preprocessed.Rd	New documentation file for `preprocessed()` generic
man/repr_S7name.Rd	Updated parameter documentation to reflect API changes
man/repr_ls.Rd	Renamed from `show_ls.Rd` with updated references
tests/testthat/test_explain.R	Changed `train()` call to use positional argument instead of named `x` parameter
tests/testthat/test_strings.R	Updated all test references from `show_ls()` to `repr_ls()`

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Copilot · 2026-01-01T12:58:48Z

tests/testthat/test_explain.R

 ## GLMET Regression ----
 mod_r_glmnet <- train(
-  x = datr_train,
+  datr_train,


The parameter name x was removed from this train() call, making it a positional argument. However, other calls to train() in this file (lines 49 and 57) still use the named parameter x = datc2_train and x = datr_train. For consistency and clarity, all calls should use the same pattern. Consider either keeping x = datr_train or updating all other calls to match this positional style.

Suggested change

datr_train,

x = datr_train,

Copilot · 2026-01-01T12:58:49Z

R/03_S7_Preprocessor.R

+method(preprocessed, Preprocessor) <- function(x) {
+  x@preprocessed
+}


The new preprocessed() generic function and its method for Preprocessor objects lack test coverage. Since other methods in the same file have comprehensive test coverage in tests/testthat/test_Preprocessor.R, consider adding a test case to verify that preprocessed(x) correctly returns the preprocessed data from a Preprocessor object.

egenn added 10 commits October 18, 2025 16:45

Merge branch 'main' into develop

13f2a92

Update comments and improve output formatting for clarity

697ad64

Add pad option to fmt()

19c67d7

up

632f1d1

use solid color for repr_S7name

aab21a8

show_ls => repr_ls

69abee2

added pad to fmt

ba8270e

Add pad parameter to highlight function for text padding

af345f4

feat: replace verbosity with prefix in repr_S7name and add `pad…

8509525

…` to `highlight`

refactor: Replace colors parameter with col and add prefix to S…

d58816d

…7 name representation functions.

gemini-code-assist bot reviewed Nov 19, 2025

View reviewed changes

R/utils_strings.R Show resolved Hide resolved

egenn added 4 commits November 19, 2025 05:25

pass prefix arg to repr_S7name

a6f88e9

added preprocessed generic and method for Preprocessor

2585b40

docs

099fc0a

0.99.1005

67e824f

gemini-code-assist bot reviewed Nov 25, 2025

View reviewed changes

R/14_S7_utils.R Outdated Show resolved Hide resolved

R/read.R Outdated Show resolved Hide resolved

egenn added 4 commits November 25, 2025 06:54

remove redundant formatting

a9f8c9a

m

c57fd40

update gray() and use instead of thin()

263ae3b

m

95e9669

Copilot AI review requested due to automatic review settings January 1, 2026 12:53

Copilot started reviewing on behalf of egenn January 1, 2026 12:54 View session

Copilot AI reviewed Jan 1, 2026

View reviewed changes

egenn added 4 commits January 8, 2026 19:37

use model.matrix on newdata

f327468

added: explain glmnet classification

be052c2

specify phi0 for regression vs. classification

99af5c3

added explain tests

5da5e29

egenn merged commit b69daa9 into main Jan 8, 2026
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egenn commented Nov 19, 2025

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