Make generation the default CLI action, copy via a switch - #48
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Pull request overview
Makes code generation the default CLI action and exposes base-class copying through --copy-base-classes.
Changes:
- Replaces CLI subcommands with a default generation workflow.
- Adds validation and tests for required/exclusive SBML arguments.
- Updates usage documentation and packaging comments.
Reviewed changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
README.md |
Documents the revised CLI. |
pyproject.toml |
Updates the package-data comment. |
chaste_sbml/__main__.py |
Implements the flat CLI interface. |
chaste_sbml/tests/test_cli.py |
Updates in-process CLI tests. |
chaste_sbml/tests/test_console.py |
Updates console integration tests. |
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Flatten the generate/copy-base-classes subcommands introduced in #39 back to a single command: generating from an SBML file is the default, and --copy-base-classes switches to copying the C++ base classes instead. The SBML file becomes an optional positional; an SBML file is required unless --copy-base-classes is given, and --copy-base-classes rejects a stray SBML file. Update the CLI tests, the README usage section, and the pyproject.toml comment to match. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Copy mode takes only --output-dir, but the flat parser accepted and silently ignored generation-only options (--model-type, --tests, --timescale, --test-output-dir). Give those options default=SUPPRESS so a missing attribute reliably means "not supplied", then report a usage error in copy mode when an SBML file or any of them is passed, and fill in the real defaults when generating. Restore the rejection test and document the behaviour. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Follow-up to enhance #39.
chaste-sbml FILE ...should generate by default without having to add ageneratesub-command. Use a--copy-base-classesswitch to emit the base classes instead of an extracopy-base-classessubcommand.