- fixed bug where rBlast temporary files were left inside working dir…

[kaozkai]

Bug description

When running ClustIRR::clustirr(), multiple database index files (.pdb, .phd, .phi, .phr, .pin, .pog, .pot, .psq, .ptf, .pto) are left behind in the user's current working directory ( getwd() ).

Supposed cause of bug

This is caused by the BLAST calling logic in blast_utils.R using basename(), which causes unlink to fail somehow.

Proposed solution

Create sandbox folders to manage tmp files and on.exit() logic to clean them up.

Summary by CodeRabbit

• Bug Fixes

  • Improved cleanup of temporary files created during BLAST-based scoring.
  • Prevented temporary artifacts from being left behind after processing.

• Tests

  • Added coverage to verify temporary files are removed.
  • Updated test data to use the current ClustIRR dataset.

[coderabbitai]

Walkthrough

get_score now stores BLAST intermediates in a dedicated temporary sandbox and removes it on exit. Tests use D1 data and verify that rBLAST temporary files do not remain in the working directory.

Changes

BLAST temporary-file cleanup

Layer / File(s)	Summary
Sandboxed BLAST artifacts and cleanup validation R/blast_utils.R, tests/testthat/test-cdr3_na.R	get_score creates and recursively removes a temporary sandbox for FASTA and BLAST database files. Tests use D1$s input and check for leftover rBLAST-style files.

Estimated code review effort: 2 (Simple) | ~10 minutes

Suggested reviewers: snaketron

Poem

A bunny tucked the BLAST files away,
In a sandbox snug for the day.
They ran, scored, and hopped,
Then the sandbox was dropped—
No stray little files left to stay.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title matches the main change: fixing rBlast temporary files left in the working directory.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch patch_rblast_index_file_cleanup

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[coderabbitai]

Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@R/blast_utils.R`:
- Around line 57-63: Update get_score_pair() in R/blast_utils.R to create a
per-call sandbox for its FASTA and BLAST database artifacts, register top-level
on.exit() cleanup, and stop writing tmp.fasta or db/tmp in the caller’s working
directory; extend tests/testthat/test-cdr3_na.R at lines 37-40 to run this path
in an isolated working directory and recursively verify no artifacts remain.

In `@tests/testthat/test-cdr3_na.R`:
- Around line 37-40: Update the cleanup assertion in test-cdr3_na.R to execute
within a fresh temporary working directory, isolating it from pre-existing
files, and make list.files scan recursively so nested rBlast artifacts are
detected. Preserve the existing BLAST-extension filter while asserting that no
matching files remain.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro Plus

Run ID: b9d348dd-59ec-4990-b8f4-ade6dd40dda5

📥 Commits

Reviewing files that changed from the base of the PR and between a562a19 and 0ec83f1.

📒 Files selected for processing (2)

• R/blast_utils.R
• tests/testthat/test-cdr3_na.R