Fixes

[Keats]

No description provided.

[Copilot]

Pull request overview

This PR improves NONMEM model/output parsing robustness and error reporting by (1) making parser diagnostics path-aware and (2) handling comma-separated table rows / FORMAT specs that include commas.

Changes:

• Updated nonmem-parser to render diagnostics with file context and to parse $TABLE ... FORMAT=,1PE15.9 correctly.
• Added a shared table-row splitter to support comma-separated (and mixed) .ext/.shk table rows without breaking parameter names like OMEGA(2,1).
• Added a comma-separated .ext fixture + snapshot updates, and adjusted some extraction tests/snapshots.

Reviewed changes

Copilot reviewed 30 out of 30 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/main.rs	Passes model path into parsing to enable path-aware diagnostics.
components/nonmem/test_data/ext/commas.ext	New .ext fixture exercising comma-separated table output.
components/nonmem/src/run/setup.rs	Switches to new Model::parse(path, input) API.
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_parse_ext_files@commas.ext.snap	New snapshot validating CSV rendering for commas.ext.
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_extract_parameter_estimates@itsimp.ext.snap	Removed snapshot (tests no longer generate per-file extraction snapshots).
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_extract_parameter_estimates@1002c.ext.snap	Removed snapshot (tests no longer generate per-file extraction snapshots).
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_extract_parameter_estimates.snap	Snapshot metadata updated after test changes.
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_extract_parameter_estimates_hiding_off_diags@itsimp.ext.snap	Removed snapshot (tests no longer generate per-file extraction snapshots).
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_extract_parameter_estimates_hiding_off_diags@1002c.ext.snap	Removed snapshot (tests no longer generate per-file extraction snapshots).
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_extract_parameter_estimates_hiding_off_diags.snap	Snapshot metadata updated after test changes.
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_extract_estimation_results@itsimp.ext.snap	Removed snapshot (tests no longer generate per-file extraction snapshots).
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_extract_estimation_results@1002c.ext.snap	Removed snapshot (tests no longer generate per-file extraction snapshots).
components/nonmem/src/output_files/snapshots/nonmem__output_files__ext__tests__can_extract_estimation_results.snap	Snapshot metadata updated after test changes.
components/nonmem/src/output_files/shk.rs	Uses shared row-splitting to parse .shk data rows more robustly.
components/nonmem/src/output_files/parsing.rs	Adds split_table_row and routes header/value parsing through it.
components/nonmem/src/output_files/mod.rs	Switches to new Model::parse(path, input) API.
components/nonmem/src/output_files/lst.rs	Threads file path into extracted-model parsing for better diagnostics.
components/nonmem/src/output_files/grd.rs	Updates tests to use new Model::parse(path, input) API.
components/nonmem/src/output_files/ext.rs	Narrows some extraction tests to a single fixture; keeps glob-based CSV snapshots for parsing.
components/nonmem/src/copy.rs	Switches to new Model::parse(path, input) API.
components/nonmem/src/check.rs	Switches to new Model::parse(path, input) API.
components/nonmem-parser/test_data/everything.mod	Adds $TABLE ... FORMAT=,1PE15.9 to cover FORMAT parsing.
components/nonmem-parser/src/snapshots/nonmem_parser__parser__tests__can_parse_mod_files@everything.mod.snap	Updates CST snapshot to reflect FORMAT tokenization.
components/nonmem-parser/src/snapshots/nonmem_parser__lower__tests__can_lower@everything.mod.snap	Updates lowered snapshot to include FORMAT option text.
components/nonmem-parser/src/parser.rs	Special-cases FORMAT values to allow leading separators/commas/parens.
components/nonmem-parser/src/model/parameters.rs	Updates tests to use inner_parse after parse API change.
components/nonmem-parser/src/model/mod.rs	Introduces inner_parse and changes public parse to be path-aware and return anyhow::Result.
components/nonmem-parser/src/model/estimates.rs	Updates tests to use inner_parse after parse API change.
components/nonmem-parser/src/model/copy.rs	Updates tests to use inner_parse after parse API change.
components/nonmem-parser/src/lower.rs	Ensures FORMAT key-values can span multiple tokens when lowering.

---

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

[Copilot]

Pull request overview

Copilot reviewed 30 out of 30 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

components/nonmem/src/output_files/ext.rs:873

• can_extract_estimation_results now only snapshots output for bql.ext, whereas previously it exercised the extraction pipeline across all EXT fixtures. Since estimation-results extraction depends on optional fields (condition number, termination codes, SD/Corr, multi-table runs), keeping coverage for at least one additional fixture like itsimp.ext (multi-method) and/or 1002c.ext (different random-effects layout) would help prevent regressions.

    #[test]
    fn can_extract_estimation_results() {
        let reader = ExtReader::default()
            .final_estimates_and_stderr_and_fixed()
            .with_condition_number()
            .with_termination_codes()
            .with_sd_corr()
            .keep_all_tables();
        let path = PathBuf::from(env!("CARGO_MANIFEST_DIR")).join("test_data/ext/bql.ext");
        let result = get_estimation_results(&path, &reader, None, false, None).unwrap();
        assert_snapshot!(format!("{:#?}", result));
    }