chore: Cleanup unused files and code

[mhovd]

No description provided.

[Copilot]

Pull request overview

This PR removes unused/legacy R utilities and patch-installation code, cleans up related package exports/docs, and bumps Rust workspace dependencies; it also reduces repeated report warnings by tracking “warn once” state per R session.

Changes:

• Bump Rust dependency versions (notably pmcore) and refresh Cargo.lock.
• Remove legacy R utilities and the PMpatch() function + its Rd/namespace export.
• Add a session-scoped “warn once” helper for PM_report() dependency fallback warnings.

Reviewed changes

Copilot reviewed 6 out of 7 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/rust/Cargo.toml	Updates pmcore dependency version used by the Rust workspace member.
Cargo.lock	Reflects dependency resolution changes from the Rust crate updates.
R/PMutilities.R	Removes large blocks of internal/unused utility code, keeping remaining helpers.
R/PMpatch.R	Deletes legacy patch installer function that sourced remote code.
man/PMpatch.Rd	Removes documentation for the deleted PMpatch() function.
NAMESPACE	Stops exporting PMpatch.
R/PM_report.R	Adds .report_warn_once() to avoid repeating the same warning in a session.
inst/mac/install_homebrew.sh	Removes deprecated Homebrew install snippet.

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[mhovd]

@mnneely, could you evaluate the following files / functions that may be removed?

• PM_batch (users can write manual loops instead)
• PMwrk2csv.R (I can't imagine anyone using USC*PACK files now)
• NPrun.R (only provides a wrapper for backwards code, but old models won't work either way)

[Copilot]

Pull request overview

Copilot reviewed 6 out of 7 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (2)

NAMESPACE:83

• PMpatch was removed from the package API, but it is still listed in _pkgdown.yml (Utility section). This will cause pkgdown reference generation to warn/fail due to a missing topic. Remove PMpatch from _pkgdown.yml (or replace it with the new equivalent, if any).

export(PMload)
export(PMmatrixRelTime)
export(PMnews)
export(PMreadDefaults)

R/PMutilities.R:5

• dmv_norm() uses p in default argument values (mean = rep(0, p), sigma = diag(p)), but p is only computed inside the function body. This will error if dmv_norm() is called without explicitly providing mean/sigma. Use NULL defaults and set them after computing p.

dmv_norm <- function(
  x, mean = rep(0, p), sigma = diag(p), log = FALSE,
  checkSymmetry = TRUE
) {

[Copilot]

Pull request overview

Copilot reviewed 7 out of 8 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

NAMESPACE:84

• PMpatch was previously an exported public function; removing its export (and deleting its implementation/docs) is a breaking API change for downstream users. If the intent is to retire the HTTP-based patch mechanism, consider keeping PMpatch() as a deprecated stub for at least one release (e.g., call .Deprecated() and/or cli::cli_abort() with a pointer to the new approach) and add a NEWS entry describing the removal.

export(PMload)
export(PMmatrixRelTime)
export(PMnews)
export(PMreadDefaults)
export(PMreport)

[Copilot]

Pull request overview

Copilot reviewed 7 out of 8 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

R/PMutilities.R:5

• dmv_norm()'s default arguments reference p, but p is only defined inside the function body. Calling dmv_norm(x) without explicitly providing mean/sigma will error when evaluating the defaults. Use NCOL(x) (or similar) in the defaults so they can be computed from x.

dmv_norm <- function(
  x, mean = rep(0, p), sigma = diag(p), log = FALSE,
  checkSymmetry = TRUE
) {

[Copilot]

Pull request overview

Copilot reviewed 9 out of 10 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

NAMESPACE:83

• Removing the exported PMpatch() API is a breaking change for downstream code; current callers will now fail with “could not find function”. The package already uses lifecycle-based deprecation wrappers (see R/Deprecated.R, e.g. PMcheckMatrix()), so it would be more consistent to keep PMpatch() as a deprecated/defunct stub that emits a clear message (and optionally stops) rather than removing it outright.

export(PMgetCRCL)
export(PMload)
export(PMmatrixRelTime)
export(PMnews)
export(PMreadDefaults)

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 62.14%. Comparing base (54ba486) to head (f88f388).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #367      +/-   ##
==========================================
+ Coverage   61.88%   62.14%   +0.26%     
==========================================
  Files          51       50       -1     
  Lines       22409    22314      -95     
==========================================
  Hits        13868    13868              
+ Misses       8541     8446      -95     

Files with missing lines	Coverage Δ
R/PMconfig.R	100.00% <ø> (+64.28%)	⬆️
R/PMutilities.R	28.16% <ø> (+3.89%)	⬆️

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[Copilot]

Pull request overview

Copilot reviewed 9 out of 10 changed files in this pull request and generated no new comments.

[Copilot]

Pull request overview

Copilot reviewed 9 out of 10 changed files in this pull request and generated no new comments.

Suppressed comments (1)

NAMESPACE:83

• Removing the exported PMpatch() function is a user-facing API break; callers will now get a generic “could not find function” error. Since the package already uses lifecycle::deprecate_warn() wrappers for retired functions (e.g., R/Deprecated.R:10-12), consider keeping a deprecated PMpatch() stub that warns and points users to the supported update path, at least for one release cycle.

export(PMload)
export(PMmatrixRelTime)
export(PMnews)
export(PMreadDefaults)

[Copilot]

Pull request overview

Copilot reviewed 9 out of 10 changed files in this pull request and generated no new comments.