Grape

[alex-sandercock]

This pull request makes significant changes to the BIGr package, primarily focused on cleaning up the codebase and dependencies by removing several unused or unnecessary functions and packages. It also updates the package metadata and dependencies for improved clarity and maintainability.

Key changes include:

Updated madc2vcf_all and madc2vcf_targets

• It was possible for POS to be exported as scientific notation instead of integers, and for negative POS values to be present for off target SNPs.
• POS are corrected to be integers, and SNPs with a negative POS value are removed.

Removal of unused functions and dependencies

• Removed the functions allele_freq_poly, solve_composition_poly, and check_ped from the codebase and from the list of exported functions in the NAMESPACE file, as well as their associated documentation. These functions are no longer maintained or required in the package. [1] [2] [3] [4]
• Removed all imports and references to the data.table, janitor, and quadprog packages from the NAMESPACE file, as they are no longer needed after the function removals. [1] [2]

Updates to package metadata and dependencies

• Updated the DESCRIPTION file to increment the version to 0.8.1, clarify the package title and description, and clean up the list of imports and suggests to accurately reflect current dependencies. Also updated formatting and moved some entries for consistency.

These changes streamline the BIGr package by removing legacy or redundant code and ensuring that only necessary dependencies are included, which should improve maintainability and reduce potential conflicts.

[Copilot]

Pull request overview

This PR streamlines the BIGr R package by removing several legacy/public pedigree-parentage and polyploid breed-composition functions (and their tests/docs), cleaning up dependencies/metadata, and hardening VCF POS handling in madc2vcf_* outputs to avoid scientific notation and invalid/negative coordinates.

Changes:

• Enforces integer, non-negative VCF POS values and drops records with invalid POS in madc2vcf_targets() and madc2vcf_all().
• Removes unused/unmaintained exported functions (validate_pedigree, find_parentage, check_ped, allele_freq_poly, solve_composition_poly) plus associated tests and man pages.
• Updates DESCRIPTION/NAMESPACE to reflect current dependencies/exports and bumps package version.

Reviewed changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
DESCRIPTION	Updates package metadata, dependency lists, and version.
NAMESPACE	Removes exports/imports for deleted legacy functions and prunes unused imports.
R/madc2vcf_all.R	Normalizes/sanitizes POS (numeric parse, drop invalid, stable sort, format as integer).
R/madc2vcf_targets.R	Normalizes/sanitizes POS (numeric parse, drop invalid, stable sort, format as integer) and adds setNames import.
R/breedtools_functions.R	Removes legacy breedTools polyploid composition utilities.
R/check_ped.R	Removes legacy pedigree QC/correction utility.
R/find_parentage.R	Removes legacy parentage assignment utility.
R/validate_pedigree.R	Removes legacy trio validation utility.
dev/dev_history.R	Adjusts dev workflow script (now executes attachment::att_amend_desc()).
man/allele_freq_poly.Rd	Removes documentation for deleted exported function.
man/check_ped.Rd	Removes documentation for deleted exported function.
man/find_parentage.Rd	Removes documentation for deleted exported function.
man/solve_composition_poly.Rd	Removes documentation for deleted exported function.
man/validate_pedigree.Rd	Removes documentation for deleted exported function.
tests/testthat/test-breedtools_poly.R	Removes tests for deleted breedTools functions.
tests/testthat/test-check_ped.R	Removes tests for deleted check_ped().
tests/testthat/test-find_parentage.R	Removes tests for deleted find_parentage().
tests/testthat/test-validate_pedigree.R	Removes tests for deleted validate_pedigree().

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[codecov]

Codecov Report

❌ Patch coverage is 66.66667% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.11%. Comparing base (7ae6e3d) to head (0453d12).
⚠️ Report is 33 commits behind head on development.

Files with missing lines	Patch %	Lines
R/madc2vcf_all.R	66.66%	3 Missing ⚠️
R/madc2vcf_targets.R	66.66%	3 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development      #66      +/-   ##
===============================================
- Coverage        81.87%   81.11%   -0.77%     
===============================================
  Files               23       19       -4     
  Lines             2886     2277     -609     
===============================================
- Hits              2363     1847     -516     
+ Misses             523      430      -93     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.