Fix CI LaTeX PDF rendering and refine aaIndex handling

[enriquea]

This pull request introduces several improvements and fixes related to the R package's isoelectric point prediction functionality and its documentation, as well as enhancements to the CI workflow for building vignettes. The main changes are grouped into workflow improvements, code fixes, and documentation cleanup.

Workflow improvements:

• Updated the GitHub Actions workflow .github/workflows/R-CMD-check.yaml to only test on R versions 4.3, 4.4, and release, removing 4.1 and 4.2 from the test matrix for efficiency.
• Added a workflow step to install additional LaTeX packages required for building the BiocStyle vignette, ensuring successful vignette compilation in CI.

Code fixes:

• Fixed a bug in the aaIndex function in R/pISVM.R by properly vectorizing the multiplication and summation of amino acid descriptors, which should correct the calculation of the Zimmerman index.

Documentation cleanup:

• Removed several generated or auxiliary files related to the vignette build process (vignettes/pIR-concordance.tex, vignettes/pIR.aux, vignettes/pIR.bbl, vignettes/pIR.blg, vignettes/pIR.out, vignettes/pIR.toc, and vignettes/pIR.tex) to keep the repository clean and avoid tracking build artifacts. [1] [2] [3] [4] [5] [6] [7]

These changes improve the reliability of CI builds, correct a calculation in the code, and reduce repository clutter.

Summary by CodeRabbit

• Documentation

  • Removed the pIR vignette documentation covering isoelectric point prediction methods and tutorials.

• Chores

  • Updated continuous integration workflow with enhanced LaTeX package support for improved vignette building.
  • Adjusted testing configuration for R version compatibility.
  • Added git ignore patterns for intermediate build artifacts and LaTeX compilation outputs.

[coderabbitai]

📝 Walkthrough

Walkthrough

The PR removes the pIR vignette source and build artifacts, updates the R-CMD-check CI workflow to drop R 4.1/4.2 support and add LaTeX package installation for BiocStyle, updates .gitignore to exclude vignette build outputs, and refactors descriptor calculation in aaIndex to use numeric vectors instead of table/data-frame operations.

Changes

Cohort / File(s)	Summary
CI Workflow Configuration .github/workflows/R-CMD-check.yaml	Removes R versions 4.1 and 4.2 from test matrix; adds LaTeX package installation step for BiocStyle vignette support; sets error-on: "error" in check-r-package step to explicitly tighten error handling.
Build Artifact Ignore Patterns .gitignore	Adds ignore rules for LaTeX compilation artifacts (*.aux, *.bbl, *.blg, *.log, *.out, *.toc), vignette concordance files (*-concordance.tex), and vignette-generated outputs under vignettes/.
Core Logic Refactor R/pISVM.R	Modifies aaIndex descriptor calculation to convert table to numeric vector explicitly using as.vector() and sum directly, replacing previous data-frame multiplication/aggregation pattern.
Vignette Source & Build Artifacts vignettes/pIR.tex, vignettes/pIR-concordance.tex, vignettes/pIR.aux, vignettes/pIR.bbl, vignettes/pIR.blg, vignettes/pIR.toc	Removes entire pIR vignette source file (262 lines) and all associated LaTeX build artifacts, including concordance mappings, auxiliary references, bibliography entries, and table-of-contents metadata.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Poem

🐰 With whiskers twitched and hoppy cheer,
Old vignettes fade, new paths are clear,
LaTeX artifacts swept away with care,
CI workflows trimmed, R versions laid bare,
The codebase hops to cleaner ground! ✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately reflects the two main changes: CI LaTeX PDF rendering fixes and aaIndex calculation refinement.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

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

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[coderabbitai]

🧹 Nitpick comments (2)

R/pISVM.R (1)

358-361: Descriptor aggregation is fixed; consider key-aligned multiplication to prevent future silent drift.

Line 358 currently relies on positional alignment between aaTable and aaZimmermanDes$value. Indexing aaTable by aaZimmermanDes$key makes this robust if ordering changes later.

Proposed refactor

-    temp <- as.vector(aaTable) * aaZimmermanDes$value
+    counts <- as.integer(aaTable[aaZimmermanDes$key])
+    temp <- counts * aaZimmermanDes$value

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@R/pISVM.R` around lines 358 - 361, The multiplication currently assumes
positional alignment between aaTable and aaZimmermanDes$value; change the
aggregation to key-aligned lookup by indexing aaTable with aaZimmermanDes$key
(e.g., use aaTable[aaZimmermanDes$key] when building temp) so temp is computed
as the elementwise product of aaTable entries matched by key and
aaZimmermanDes$value, then sum temp into zimm as before (ensure
aaZimmermanDes$key exists and handles missing keys appropriately).

.github/workflows/R-CMD-check.yaml (1)

77-77: Consider tightening warning policy after baseline cleanup.

Line 77 currently lets warnings pass (error-on: '"error"'), which is fine as a temporary stabilization step, but it can let new quality regressions accumulate. Consider tracking current warnings and moving back to warning-level enforcement once the backlog is resolved.

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In @.github/workflows/R-CMD-check.yaml at line 77, The workflow currently sets
the R-CMD-check policy to treat only errors as failures via the "error-on"
setting (error-on: '"error"'), which allows warnings to pass; change this to
tighten the policy once the current warning backlog is cleared by switching the
"error-on" value to include warnings (for example set error-on to '"warning"')
or implement a baseline-tracking approach (store current warnings and fail only
on new warnings) and update the "error-on" configuration accordingly so new
regressions are enforced; look for the "error-on" key to update its value or add
baseline-handling logic in the workflow.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In @.github/workflows/R-CMD-check.yaml:
- Line 77: The workflow currently sets the R-CMD-check policy to treat only
errors as failures via the "error-on" setting (error-on: '"error"'), which
allows warnings to pass; change this to tighten the policy once the current
warning backlog is cleared by switching the "error-on" value to include warnings
(for example set error-on to '"warning"') or implement a baseline-tracking
approach (store current warnings and fail only on new warnings) and update the
"error-on" configuration accordingly so new regressions are enforced; look for
the "error-on" key to update its value or add baseline-handling logic in the
workflow.

In `@R/pISVM.R`:
- Around line 358-361: The multiplication currently assumes positional alignment
between aaTable and aaZimmermanDes$value; change the aggregation to key-aligned
lookup by indexing aaTable with aaZimmermanDes$key (e.g., use
aaTable[aaZimmermanDes$key] when building temp) so temp is computed as the
elementwise product of aaTable entries matched by key and aaZimmermanDes$value,
then sum temp into zimm as before (ensure aaZimmermanDes$key exists and handles
missing keys appropriately).

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 6eab422e-f19c-48e3-a7f9-befda4dee348

📥 Commits

Reviewing files that changed from the base of the PR and between 698420a and d064c26.

⛔ Files ignored due to path filters (3)

• vignettes/pIR.log is excluded by !**/*.log
• vignettes/pIR.out is excluded by !**/*.out
• vignettes/pIR.pdf is excluded by !**/*.pdf

📒 Files selected for processing (9)

• .github/workflows/R-CMD-check.yaml
• .gitignore
• R/pISVM.R
• vignettes/pIR-concordance.tex
• vignettes/pIR.aux
• vignettes/pIR.bbl
• vignettes/pIR.blg
• vignettes/pIR.tex
• vignettes/pIR.toc

💤 Files with no reviewable changes (6)

• vignettes/pIR-concordance.tex
• vignettes/pIR.aux
• vignettes/pIR.bbl
• vignettes/pIR.blg
• vignettes/pIR.tex
• vignettes/pIR.toc