Development#13
Merged
Merged
Conversation
spec snp file
Updated .ignore files and added write_par() to create a basic .par file
Updated .ignore files and added write_par() to create a basic .par file Updated NEWS and README
…development # Conflicts: # NEWS.md
There was a problem hiding this comment.
Pull request overview
This PR bumps BIGf90 to v0.4.0, adds a new write_par() helper for generating raw RENUMF90 .par files from R, and refreshes CVA/genomic workflows and package docs/tests accordingly.
Changes:
- Added
write_par()(exported + documented) and a new testthat suite coveringwrite_par()andcreate_folds(). - Updated
bf90_cv()/CV helpers to support reusing pre-built genomic artifacts (Gi + cleaned SNPs) and adjusted file handling. - Version/docs housekeeping: README badges, NEWS entry, DESCRIPTION metadata, ignore rules.
Reviewed changes
Copilot reviewed 16 out of 20 changed files in this pull request and generated 11 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/testthat/test-write_par.R | New unit tests for .par assembly behavior and error paths. |
| tests/testthat/test-utils.R | New unit tests for create_folds(). |
| tests/testthat.R | Adds testthat runner for the package. |
| README.md | Adds badges and mentions write_par(). |
| R/write_par.R | Implements write_par() to build/write raw RENUMF90 .par files. |
| R/utils.R | Updates CV helpers (mutate_folds(), create_cv_datasets()) for ID-column masking and reuse-files symlinks. |
| R/run_renum.R | Adds parameter-file validation and improves output file handling. |
| R/run_predict.R | Uses file.path() for executable path handling. |
| R/run_postgibbs.R | Moves result files to output_files_dir and adjusts log reading. |
| R/run_blup.R | Uses file.path() for executable path handling. |
| R/bf90_cv.R | Refactors CV flow, adds genomic reuse behavior, removes args (ped/snp) from signature. |
| NEWS.md | Adds v0.4.0 release notes. |
| NAMESPACE | Exports write_par. |
| man/write_par.Rd | New generated Rd for write_par(). |
| man/bf90_cv.Rd | Updates signature docs to match removed parameters. |
| inst/no_cov_script.R | Removes an old example script. |
| DESCRIPTION | Bumps version and adds testthat metadata. |
| .Rbuildignore | Expands build ignore patterns. |
| .gitignore | Cleans up ignore rules; keeps tests/ tracked. |
Files not reviewed (2)
- man/bf90_cv.Rd: Generated file
- man/write_par.Rd: Generated file
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
updated Description file
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Updated to version 0.4