Extend get_required_input_variables: Pharmpy object, data arg, bug fixes

[roninsightrx]

Summary

• Accept Pharmpy model objects in addition to file paths and code strings
• Add data argument (data.frame or CSV path) to populate data_col from actual dataset column names via positional matching; auto-detects the dataset from $DATA when omitted, with a clear warning if the file cannot be found
• Fix $INPUT rename parsing — NONMEM's rename syntax is NONMEM_NAME=DATA_COL (was reversed in .parse_nm_input)
• Relax column-count check — extra trailing data columns are trimmed rather than aborting; only warns when data has fewer columns than $INPUT entries (where positional matching would be unreliable)

Test plan

• Run devtools::test(filter = "get_required_input_variables") — covers all classification types (reserved, used/unused covariate, dose variable, dropped), data resolution paths (explicit data.frame, CSV file, $DATA auto-detect), edge cases (multi-line $INPUT, inline comments, IGNORE=C), and error conditions
• Run devtools::check() to confirm no regressions

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Adds a new exported helper for parsing NONMEM $INPUT and determining which input variables are required for simulation, with optional dataset-based resolution of data_col and expanded input types (model string/path/Pharmpy object).

Changes:

• Introduces get_required_input_variables() with internal helpers to parse $INPUT, detect dose-timing RHS variables, and optionally resolve data_col via data or $DATA.
• Adds comprehensive test coverage for classification, renames/DROP, IGNORE=C, multiline/inline-comment $INPUT, and data resolution behavior.
• Adds roxygen2 docs/man pages, exports the new API, and bumps package version.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
R/get_required_input_variables.R	New exported function + internal parsing/data-resolution helpers
tests/testthat/test-get_required_input_variables.R	New tests covering parsing, classification, and data resolution paths
man/get_required_input_variables.Rd	Public API documentation
man/dot-resolve_data_cols.Rd	Internal helper documentation
man/dot-parse_nm_input.Rd	Internal helper documentation
man/dot-find_dose_variables.Rd	Internal helper documentation
NAMESPACE	Exports get_required_input_variables
DESCRIPTION	Version bump

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[Copilot]

Tests that call get_required_input_variables(simple_code) (where simple_code contains $DATA data.csv) will typically emit a $DATA file ... not found warning because the model is passed as a code string and data.csv won’t exist in the test working directory. To keep test output clean (and avoid check notes about warnings during tests), consider removing $DATA from the in-memory snippets, creating a temporary data.csv via withr::local_dir() + write.csv(), or wrapping those calls in suppressWarnings()/expect_warning(..., NA) where appropriate.