dev UD

.Rbuildignore

@@ -1,2 +1,6 @@
 ^ReadWriter\.Rproj$
 ^\.Rproj\.user$
+^\.github$
+^Development$
+^AGENTS\.md$
+^CITATION\.cff$

.github/workflows/claude.yml

@@ -0,0 +1,25 @@
+name: Claude Code
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+jobs:
+  claude:
+    if: contains(github.event.comment.body, '@claude') || contains(github.event.issue.body, '@claude') || contains(github.event.review.body, '@claude')
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+      issues: write
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+        with: { fetch-depth: 1 }
+      - uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}

.gitignore

@@ -1,45 +1,61 @@
-# History files
+# R and RStudio local state
 .Rhistory
 .Rapp.history
-
-# Session Data files
 .RData
-
-# User-specific files
+.RDataTmp
 .Ruserdata
+.Rproj.user/
+*.Rproj
+.Renviron
 
-# Example code in package build process
-*-Ex.R
+# R serialized data
+*.rds
+*.RDS
+*.rda
+*.RData
 
-# Output files from R CMD build
+# R build and check output
+*-Ex.R
 /*.tar.gz
-
-# Output files from R CMD check
 /*.Rcheck/
-
-# RStudio files
-.Rproj.user/
-
-# produced vignettes
+*_cache/
+/cache/
+*.utf8.md
+*.knit.md
 vignettes/*.html
 vignettes/*.pdf
 
-# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+# Authentication and deployment metadata
 .httr-oauth
+rsconnect/
 
-# knitr and R markdown default cache directories
-*_cache/
-/cache/
+# Generated package documentation
+docs/
 
-# Temporary files created by R markdown
-*.utf8.md
-*.knit.md
+# Translation temporary files
+po/*~
 
-# R Environment Variables
-.Renviron
+# Accidental analysis output
+*.pdf
+*.png
+
+# Local aliases and links
+*alias
+
+# macOS Finder metadata
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+
+# Windows metadata
+Thumbs.db
+ehthumbs.db
+
+# Linux/HPC core dumps
+core
+core.*
+core-*
+*.core
 .Rproj.user
-ReadWriter.Rproj
-*.Rproj
-ReadWriter.Rproj
-ReadWriter.Rproj
-*.Rproj

AGENTS.md

@@ -0,0 +1,28 @@
+# AGENTS.md
+
+## Overview
+ReadWriter is an R package providing convenience functions for reading from and writing to text-based data files. The package aims to streamline common I/O tasks and complements other tools in the `@vertesy` ecosystem.
+
+## Repository structure
+- `R/` – source code. All exported functions live in `ReadWriter.R`; deprecated helpers are kept in `Deprecated.Functions.R`.
+- `man/` – autogenerated documentation for functions (update with `devtools::document`).
+- `Development/` – scripts used to build or maintain the package; not installed with the package.
+- `DESCRIPTION` – package metadata and dependency declarations.
+- `README.md` – installation instructions and a high-level overview.
+
+## Dependencies
+- Requires the `@vertesy` package [`Stringendo` (>=0.5.0)](https://github.com/vertesy/Stringendo) and CRAN packages `gtools`, `openxlsx`, `qs`, and `readr`.
+- Install `Stringendo` before installing ReadWriter:
+  ```r
+  devtools::install_github("vertesy/Stringendo", upgrade = FALSE)
+  ```
+- Add any new dependencies to the `Imports` field in `DESCRIPTION`.
+
+## Development guidelines
+- Place new functions in `R/ReadWriter.R` and document them with roxygen comments.
+- Run `R -q -e "devtools::document()"` to regenerate Rd files before committing.
+- Verify the package with `R -q -e "devtools::check(document = FALSE)"`; checks should pass with no errors.
+- There is currently no automated test suite. Manual testing of new functionality is encouraged.
+
+## Getting started
+New contributors should read `README.md` for installation details and review `R/ReadWriter.R` to understand available functions. For broader context and utility helpers, explore the `Stringendo` package and other repositories in the `@vertesy` organization.

CITATION.cff

@@ -1,12 +1,12 @@
 cff-version: 1.2.0
 title: vertesy/ReadWriter Functions to read and write tabular data files conveniently.
-version: v1.6.1
+version: v1.6.9
 message: >-
   If you use this software, please cite it using these metadata.
 type: software
 authors:
   - given-names: Abel
     family-names: Vertesy
-    email: abel.vertesy@imba.oeaw.ac.at
+    email: av@imba.oeaw.ac.at
     affiliation: IMBA
     orcid: 'https://orcid.org/0000-0001-6075-5702'

DESCRIPTION

@@ -1,11 +1,10 @@
 Package: ReadWriter
 Title: ReadWriter
-Version: 1.6.1
+Version: 1.6.9
 Authors@R: 
     person("Abel", "Vertesy", , "av@imba.oeaw.ac.at", role = c("aut", "cre"))
-Author: Abel Vertesy <av@imba.oeaw.ac.at> [aut, cre]
 Description: ReadWriter is a set of R functions to read and write files
-    conveniently. Complements CodeAndRoll2.
+    conveniently. Builds on Stringendo and complements CodeAndRoll2.
 License: GPL-3 + file LICENSE
 BugReports: https://github.com/vertesy/ReadWriter/issues
 Depends: 
@@ -16,6 +15,6 @@ Imports:
     qs,
     readr
 Encoding: UTF-8
-Packaged: 2025-07-14 12:49:22.339709
+Packaged: 2026-08-25 16:41:37.734198
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

Development/Create_the_ReadWriter_Package.R

@@ -27,8 +27,8 @@ devtools::install_local(repository.dir, upgrade = F)
 
 
 # Test if you can install from github ------------------------------------------------
-remote.path <- file.path(DESCRIPTION$'github.user', package.name)
-pak::pkg_install(remote.path)
+# remote.path <- file.path(DESCRIPTION$'github.user', package.name)
+# pak::pkg_install(remote.path)
 
 devtools::install_github(repo = "vertesy/Seurat.utils", upgrade = F)
 
@@ -46,7 +46,6 @@ devtools::check_man(repository.dir)
 checkres <- devtools::check(repository.dir, cran = FALSE)
 
 
-
 # Automated Codebase linting to tidyverse style ------------------------------------------------
 styler::style_pkg(repository.dir)
 
@@ -85,11 +84,11 @@ if (F) {
 for (scriptX in ls.scripts.full.path) {
   PackageTools::list_of_funs_to_markdown(scriptX)
 }
-file.edit(paste0(repository.dir, "R/list.of.functions.in.", package.name, ".det.md"))
-file.edit(paste0(repository.dir, "README.md"))
+file.edit(paste0(repository.dir, "/R/list.of.functions.in.", package.name, ".det.md"))
+file.edit(paste0(repository.dir, "/README.md"))
 file.remove(paste0(repository.dir, "/R/list.of.functions.in.", package.name, ".det.md"))
 
-r$PackageTools()
+d$PackageTools()
 PackageTools::copy_github_badge("active") # Add badge to readme via clipboard
 file.edit(paste0(repository.dir, "README.md"))