Add support for rtemis.server

[egenn]

No description provided.

[gemini-code-assist]

Code Review

This pull request introduces a progress callback argument to the train() function to support non-interactive progress tracking, adds a new generic get_varimp for retrieving variable importance, and updates several S7 class definitions and validation helpers. The feedback highlights two key improvements: first, using length(outer_resampler@resamples) instead of outer_resampler@config@n to robustly determine the number of outer folds; second, reverting the use of let() to := in R/draw_box.R to maintain backward compatibility with older versions of data.table since no minimum version is specified in the package description.

[Copilot]

Pull request overview

This PR appears to improve compatibility with non-interactive callers (notably rtemis.server) by adding an explicit training progress callback, tightening/standardizing S7 class metadata, and introducing a small exported API for variable-importance retrieval.

Changes:

• Add an optional progress(stage, current, total, message) callback to train() and wire it into the outer resampling loop.
• Introduce and export a new get_varimp() S7 generic with methods for Supervised / SupervisedRes.
• Standardize multiple S7 new_class() definitions by setting package = "rtemis" and adjust dependency/check helpers (add rtemis.core).

Reviewed changes

Copilot reviewed 23 out of 25 changed files in this pull request and generated 21 comments.

Show a summary per file

File	Description
R/train.R	Adds progress callback argument and emits fold-boundary progress events during outer resampling.
R/draw_box.R	Attempts to avoid mutating dt before melt() by switching from := to let().
R/decomp.R	Header comment tweak.
R/16_S7utils.R	Header comment tweak.
R/14_SuperConfig.R	Adds package = "rtemis" to S7 classes; modifies roxygen block near class defs.
R/13_Themes.R	Adds package = "rtemis" to S7 class; modifies roxygen block near class def.
R/12_Decomposition.R	Adds package = "rtemis" to S7 class; modifies roxygen block near class def.
R/11_DecompositionConfig.R	Adds package = "rtemis"; swaps numeric checks to rtemis.core::check_numeric().
R/10_Clustering.R	Adds package = "rtemis"; modifies roxygen block near class def.
R/09_ClusteringConfig.R	Adds package = "rtemis"; swaps numeric checks to rtemis.core::check_numeric().
R/08_MassUni.R	Adds package = "rtemis" and adjusts class documentation tags.
R/07_Supervised.R	Adds package = "rtemis" to several classes and adds get_varimp methods.
R/06_Tuner.R	Adds package = "rtemis"; modifies roxygen block near class defs.
R/05_Resampler.R	Adds package = "rtemis"; modifies roxygen block near class defs.
R/04_Preprocessor.R	Adds package = "rtemis"; modifies roxygen block near class defs.
R/03_Metrics.R	Adds package = "rtemis"; modifies roxygen block near class def.
R/02_Hyperparameters.R	Adds package = "rtemis"; swaps numeric checks to rtemis.core::check_numeric().
R/01_ExecutionConfig.R	Adds package = "rtemis"; modifies roxygen block near class def.
R/00_S7init.R	Defines/export get_varimp S7 generic and roxygen docs/examples.
NAMESPACE	Exports get_varimp.
man/train.Rd	Documents new progress argument.
man/get_varimp.Rd	Adds generated documentation for get_varimp.
Makefile	Changes log timestamp formatting.
DESCRIPTION	Bumps version/date; adds rtemis.core to Imports; removes plumber from Suggests.
.Rbuildignore	Removes one ignore entry; adds ignore pattern for PDFs.

Files not reviewed (2)

• man/get_varimp.Rd: Language not supported
• man/train.Rd: Language not supported

Comments suppressed due to low confidence (1)

R/draw_box.R:972

• dt[, let(ID = .I)] does not preserve the existing columns of dt, so data.table::melt() will likely fail because id.vars includes columns like timeperiod/group/hovertext that are no longer present. To avoid mutating dt while keeping all columns, use something like copy(dt)[, ID := .I] (or add ID then remove it after melting).

    # appease R CMD check ?rm timeperiod <- NULL
    ID <- timeperiod <- NULL
    dtlong <- data.table::melt(
      dt[, let(ID = .I)],
      id.vars = c(
        "ID",
        "timeperiod",
        mgetnames(dt, "group", "hovertext")
      )
    )

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