[alex-sandercock]

This pull request releases version 0.13.0 of MADCATS and makes significant improvements to the documentation and command-line interface, while removing legacy compatibility code. The key changes include clearer and more consistent command-line help, improved documentation links and descriptions, and the removal of the deprecated madc_pipeline.py compatibility shim. The documentation now references a single development record on GitHub, and several option descriptions and defaults have been clarified.

Major changes by theme:

Removal of legacy compatibility code

• Removed the madc_pipeline.py compatibility module; users and scripts should now import or invoke madcats directly. (madc_pipeline.py)

Command-line interface improvements

• All commands now have clear descriptions and help text for every option. Usage lines consistently refer to the program as madcats. (madcats.py) [1] [2] [3] [4] [5] [6]
• The --partial-read-mode option now uses on/off values for consistency with other switches; the old assign value is still accepted as on with a warning. (madcats.py)
• Improved help and descriptions for design, infer-design, and merge-pairs commands, making their purpose and arguments clearer. (madcats.py) [1] [2] [3]

Documentation and changelog updates

• Updated the documentation to reference the development record on GitHub instead of the previous "Development Reference" or local files. This affects the README, changelog, evidence model, validation, and contributing guidelines. (README.md, docs/src/development/changelog.md, docs/src/reference/evidence-model.md, docs/src/reference/validation.md, docs/src/development/contributing.md) [1] [2] [3] [4] [5]
• Removed the inclusion of the development reference from the published documentation and updated the summary and navigation accordingly. (docs/src/SUMMARY.md, docs/src/development/reference.md) [1] [2]

Option and version updates

• Updated the version number to 0.13.0 throughout the code and documentation. (madcats.py, docs/src/citation.md, docs/src/getting-started/installation.md) [1] [2] [3]
• Clarified and updated option descriptions and defaults for --partial-read-mode, denoising distances, and related options in both the help text and documentation. (docs/src/commands/generate.md, docs/src/development/changelog.md, docs/DEVELOPMENT.md, docs/src/reference/evidence-model.md) [1] [2] [3] [4] [5]

Minor cleanups

• Removed references to the now-removed compatibility shim and updated architecture documentation accordingly. (docs/src/development/architecture.md, docs/src/commands/generate.md) [1] [2]
• Various minor clarifications and rewordings across documentation and changelog. (Multiple references above)

[Copilot]

🟢 Approval recommended

The CLI transition, import migrations, packaging cleanup, and documentation updates are consistent, with no unresolved blocking issues.

No open issues 🎉

What changed in this PR

Prepares MADCATS 0.13.0 with clearer command-line guidance, updated documentation, and removal of the legacy module name.

Changes:

• Expands command help and standardizes --partial-read-mode to on/off, preserving assign with a warning.
• Removes the compatibility shim and migrates bundled scripts and packaging to madcats.
• Updates version references and links documentation to the GitHub development record.

File	Description
tests/​test_madcats.py	Updates partial-read tests and checks the legacy alias.
scripts/​validate_inferred_design.py	Imports directly from madcats.
scripts/​madc_to_reference_tags.py	Imports directly from madcats.
scripts/​analyze_extra_quality.py	Imports directly from madcats.
scripts/​analyze_dart_only.py	Imports directly from madcats.
scripts/​analyze_count_vector_matches.py	Imports directly from madcats.
README.md	Links to the GitHub development record.
pyproject.toml	Removes the compatibility module from packaging.
madcats.py	Updates version, CLI help, and partial-read option handling.
madc_pipeline.py	Deletes the legacy compatibility shim.
docs/​src/​SUMMARY.md	Removes the development-reference navigation entry.
docs/​src/​reference/​validation.md	Links validation history to the development record.
docs/​src/​reference/​evidence-model.md	Updates the development link and denoising wording.
docs/​src/​getting-started/​installation.md	Updates the example version output.
docs/​src/​development/​reference.md	Removes the embedded development record.
docs/​src/​development/​contributing.md	Links directly to the development record.
docs/​src/​development/​changelog.md	Documents 0.13.0 and clarifies release history.
docs/​src/​development/​architecture.md	Removes the compatibility-shim entry.
docs/​src/​commands/​generate.md	Updates option values and denoising descriptions.
docs/​src/​citation.md	Updates the methods example to 0.13.0.
docs/​DEVELOPMENT.md	Removes the obsolete compatibility-shim statement.

_{Review effort: Balanced}