Mini cleanup

[pdiakumis]

• Tool:
  • make input_id, output_id optional
  • keep raw file path in write result, for use within metadata
• Workflow:
  • use metapkg field for specifying pkgs for metadata versioning
  • enhance printer with file count (total vs. pattern-matching)
• Metadata:
  • make input_id, output_id optional
  • write to _metadata/metadata.json now
• Add nemo_schema_check (converted this to a function from a Claude skill, want to build on top of this at some point)
• nemo_schema_data -> nemo_schemavis_data for clarity

[Copilot]

Pull request overview

This PR performs a small API/UX cleanup across the core Tool/Workflow write + metadata flow, updates schema-visualization naming, and introduces a new schema validation helper (nemo_schema_check) to validate schema.yaml structure and conventions.

Changes:

• Make input_id / output_id optional in Tool$write() and Workflow$write(), and include the raw input file path (raw_path) in write results for metadata.
• Adjust workflow metadata behavior: add metapkg to control which package(s) are version-reported, and write metadata into an _metadata/metadata.json subdirectory.
• Add nemo_schema_check() and rename nemo_schema_data() → nemo_schemavis_data() across code/docs/tests.

Reviewed changes

Copilot reviewed 11 out of 17 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
vignettes/fig/uml/nemo.uml	Removes PlantUML source from vignettes UML assets.
vignettes/fig/uml/nemo.svg	Removes generated SVG UML diagram from vignettes UML assets.
tests/testthat/test-roxytest-testexamples-schema_vis.R	Updates generated roxytest expectations for renamed schema-vis data function.
tests/testthat/test-roxytest-testexamples-schema_check.R	Adds generated roxytest coverage for new nemo_schema_check().
R/Workflow.R	Adds metapkg, updates printing, makes IDs optional, writes metadata under _metadata/, and adjusts metadata file manifest fields.
R/Tool.R	Makes IDs optional in write(), adds raw_path to write output, and updates list_files documentation wording.
R/schema_vis.R	Renames nemo_schema_data() to nemo_schemavis_data() and updates reactable helper usage.
R/schema_check.R	Introduces new schema validation function and internal checker.
R/metadata.R	Updates metadata title/fields and loosens type checks for optional IDs.
NAMESPACE	Exports new nemo_schema_check and renamed nemo_schemavis_data; drops export of old name.
man/Workflow.Rd	Documents new metapkg, optional output_id, and updated list_files description.
man/Tool.Rd	Documents optional output_id and updated list_files description.
man/reactable_schema.Rd	Updates example to call nemo_schemavis_data().
man/nemo_schemavis_data.Rd	Updates generated Rd for renamed schema-vis data function.
man/nemo_schema_check.Rd	Adds generated Rd for new schema check function.
man/nemo_metadata.Rd	Updates title/description for metadata helper.
.claude/CLAUDE.md	Refreshes contributor guidance and the API reference table (but still contains an outdated function name reference).

Files not reviewed (5)

• man/Tool.Rd: Language not supported
• man/Workflow.Rd: Language not supported
• man/nemo_metadata.Rd: Language not supported
• man/nemo_schema_check.Rd: Language not supported
• man/reactable_schema.Rd: Language not supported

Comments suppressed due to low confidence (1)

R/Tool.R:577

• Tool$write() now returns a raw_path column, but the method’s return-value documentation (and any roxytest expectations generated from it) still describe the old column set. Update the roxygen/Rd docs (and any @testexamples that assert the column names) to include raw_path so the public API remains accurate.

        dplyr::select(
          "raw_path",
          "tool_parser",
          "prefix",
          "tidy_data",
          "tbl_name",
          "outpath"
        )

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