Release rbi 1.0.1

[sbfnk]

Patch release fixing character column handling in sparse input data.

Closes #55, closes #57.

Changes

• Fix handling of character columns in sparse input data (turn character vectors into factors #54)
• Improve error messages when LibBi fails (include exit code and stderr)
• Work around upstream LibBi assertion bug in tests
• Update deprecated GitHub Actions to v4
• Fix moved URL in vignette
• Add missing na.omit import to NAMESPACE
• Add .claude to .Rbuildignore
• Update cran-comments.md for current test environments

[codecov]

Codecov Report

❌ Patch coverage is 80.00000% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 97.06%. Comparing base (2de0f5e) to head (c06a7db).
⚠️ Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
R/libbi.R	73.68%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #58      +/-   ##
==========================================
- Coverage   97.34%   97.06%   -0.28%     
==========================================
  Files          17       17              
  Lines        1735     1740       +5     
==========================================
  Hits         1689     1689              
- Misses         46       51       +5     

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[Copilot]

Pull request overview

Patch release prep for rbi 1.0.1, focusing on more robust handling of character columns (by normalizing them to factors) when writing/attaching sparse NetCDF input data, plus standard CRAN/release housekeeping.

Changes:

• Normalize character columns to factors when writing NetCDF data (bi_write()) and when libbi() processes list-based init/input/obs options.
• Release housekeeping: bump version/roxygen note, update NEWS/CRAN comments, ignore .claude, refresh GitHub Actions checkout versions, and fix a vignette URL.

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
R/bi_write.R	Adds internal helpers to gather character levels and factorise character columns before writing NetCDF.
R/libbi.R	Ensures list-based file options have consistent factor levels; tweaks attach_data() time guessing behavior; removes explicit return() usage in several places.
man/get_char_levels.Rd	New internal documentation for get_char_levels().
man/factorise.Rd	New internal documentation for factorise().
NAMESPACE	Adds missing stats::na.omit import.
NEWS.md	Updates release notes for 1.0.1.
DESCRIPTION	Bumps package version to 1.0.1 and updates RoxygenNote.
vignettes/rbi.Rmd	Updates a NetCDF URL.
cran-comments.md	Updates test environment reporting for CRAN submission.
.Rbuildignore	Adds .claude to build ignore list.
.github/workflows/test-coverage.yaml	Updates actions/checkout/upload-artifact to v4.
.github/workflows/render_readme.yml	Updates actions/checkout to v4.
.github/workflows/lint_changed_files.yaml	Updates actions/checkout to v4.
.github/workflows/_pkgdown.yml	Updates actions/checkout to v4.
.github/workflows/R-CMD-check.yaml	Updates actions/checkout to v4.
.github/workflows/R-CMD-check-docker.yaml	Updates actions/checkout to v4.

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Walkthrough

This PR prepares the RBi package for release 1.0.1, updating package metadata and dependencies, enhancing error handling in the LibBi runner, refactoring function returns, and documenting character column handling improvements in sparse data processing.

Changes

Cohort / File(s)	Summary
GitHub Actions Workflows .github/workflows/R-CMD-check-docker.yaml, .github/workflows/R-CMD-check.yaml, .github/workflows/_pkgdown.yml, .github/workflows/lint_changed_files.yaml, .github/workflows/render_readme.yml, .github/workflows/test-coverage.yaml	Updated action versions: checkout@v3/v2 → @v4, upload-artifact@v3 → @v4. Added OMP_NUM_THREADS environment variable in R-CMD-check workflow.
Package Metadata DESCRIPTION, NAMESPACE, NEWS.md	Version bumped to 1.0.1, Roxygen updated to 7.3.3, importFrom(stats, na.omit) added, release notes updated documenting character column handling in sparse data.
Build & Configuration .Rbuildignore, .coderabbit.yaml, codecov.yml	Added .claude ignore pattern, new CodeRabbit config enabling request_changes_workflow, codecov patch coverage disabled.
R Core Functions R/bi_write.R, R/libbi.R	Removed explicit return statements for implicit returns; enhanced error handling in run.libbi to distinguish between explicit error messages and exit codes with stderr logging.
Documentation man/factorise.Rd, man/get_char_levels.Rd	Added Rd documentation files for factorise and get_char_levels helper functions.
Release & Test Updates cran-comments.md, tests/testthat/test-libbi.r, vignettes/rbi.Rmd	Updated CRAN comments with test environments, simplified check results summary, changed test flag from --enable-assert to --verbose, corrected NetCDF documentation link.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~22 minutes

Poem

🐰 Version one-point-one hops into view,
Sparse data's characters transform through and through,
Returns flow implicit, workflows are bright,
Error messages clearer from day into night—
A release refined with a twitchy-nosed delight!

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Release rbi 1.0.1' accurately summarizes the main objective of the PR: preparing and releasing version 1.0.1 of the rbi package.
Linked Issues check	✅ Passed	The PR successfully addresses all coding-related requirements from linked issues #55 and #57: bug fixes for character columns in sparse data and dimension ordering, updated GitHub Actions to v4, fixed vignette URL, added na.omit import, updated .Rbuildignore, version bump to 1.0.1, and cran-comments updates.
Out of Scope Changes check	✅ Passed	All changes align with the release preparation scope: bug fixes, dependency updates, configuration updates, and documentation/metadata changes directly support the version 1.0.1 release objectives outlined in issues #55 and #57.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@NEWS.md`:
- Around line 1-4: Add a second changelog bullet under "rbi 1.0.1" documenting
the dimension-ordering bug fix: state that the ordering of dimensions when
writing init files for multi-dimensional parameters during chaining was
corrected (i.e., fixed initialization file dimension ordering for chained
sampling), and reference the associated issue/PR number if available so users
see both fixes in the release notes.

🧹 Nitpick comments (2)

cran-comments.md (1)

2-4: Test environments updated appropriately for the submission.

The environments cover macOS (local + CI) and Windows (win-builder devel), which is a reasonable spread. Consider whether adding a Linux environment entry (e.g., from the R-CMD-check GitHub Actions workflow) would strengthen the CRAN submission, since the CI clearly runs on ubuntu-latest as well.

R/bi_write.R (1)

499-514: Minor: factorise modifies variables in a loop over column names—consider potential redundant iterations.

When multiple columns need factorisation, lapply over all data_frames runs for each column in names(levels). If a given data frame has many columns to convert, each lapply pass rewrites the entire list. For typical LibBi usage with a small number of factor columns this is fine, but be aware it's O(cols × data_frames) list replacements.

The logic itself is correct—the col %in% colnames(df) guard safely skips data frames that don't contain the column.