Clarify verbose messaging and print control

AGENTS.md

@@ -0,0 +1,36 @@
+# AGENTS
+
+## Overview
+This repository contains the **CodeAndRoll2** R package, a collection of utility functions for vector, matrix, and list manipulations.
+
+### Structure
+- `R/` – core package functions.
+  - `CodeAndRoll2.R` exposes the main utilities.
+  - `deprecated.R` lists legacy helpers that should not be used in new code.
+- `man/` – roxygen2-generated documentation.
+- `DESCRIPTION` & `NAMESPACE` – package metadata.
+- `Development/` – auxiliary scripts used for building and maintenance; not required for package use.
+- `README.md` – package description, installation instructions, and an extensive function catalogue.
+
+## Development Workflow
+1. Use R (>= 4.0).
+2. After editing code in `R/`, keep roxygen2-style comments and regenerate documentation with:
+   ```r
+   devtools::document()
+   ```
+3. Run checks before committing:
+   ```sh
+   R CMD build .
+   R CMD check CodeAndRoll2_*.tar.gz
+   ```
+   (or in R: `devtools::check()`).
+4. Delete the generated `CodeAndRoll2_*.tar.gz` archive and `CodeAndRoll2.Rcheck` directory after the check.
+5. Commit only when checks complete without errors or warnings.
+
+## Getting Started for New Contributors
+- Read `README.md` for a package overview and list of available functions.
+- Explore `R/CodeAndRoll2.R` to see implementation style and naming conventions.
+- Review `DESCRIPTION` to understand package dependencies (e.g., Stringendo, ReadWriter).
+- Check `deprecated.R` to avoid relying on obsolete functions.
+- Suggested next steps: learn roxygen2 for documentation, devtools for package development, and review dependent packages (MarkdownReports, ggExpress, Seurat.utils) to see CodeAndRoll2 in action.
+

Development/zacc/CodeAndRoll2.orig.R

@@ -275,7 +275,7 @@ zigzagger <- function(vec = 1:9) { # mix entries so that they differ
   intermingle2vec(vec, rev(vec))[1:length(vec)]
 }
 
-numerate <- function(x = 1, y = 100, zeropadding = TRUE, pad_length = floor( log10( max(abs(x), abs(y)) ) ) + 1) { # numerate from x to y with additonal zeropadding
+numerate <- function(x = 1, y = 100, zeropadding = TRUE, pad_length = floor( log10( max(abs(x), abs(y)) ) ) + 1) { # numerate from x to y with additional zeropadding
   z = x:y
   if (zeropadding) { z = stringr::str_pad(z, pad = 0, width = pad_length)   }
   return(z)

Development/zacc/oxy-CodeAndRoll2.orig.R

@@ -854,7 +854,7 @@ zigzagger <- function(vec = 1:9) { # mix entries so that they differ
 #' @rdname numerate
 #' @export 
 #' @importFrom stringr str_pad
-numerate <- function(x = 1, y = 100, zeropadding = TRUE, pad_length = floor( log10( max(abs(x), abs(y)) ) ) + 1) { # numerate from x to y with additonal zeropadding
+numerate <- function(x = 1, y = 100, zeropadding = TRUE, pad_length = floor( log10( max(abs(x), abs(y)) ) ) + 1) { # numerate from x to y with additional zeropadding
   z = x:y
   if (zeropadding) { z = stringr::str_pad(z, pad = 0, width = pad_length)   }
   return(z)