Retire metpo/presentations/ analysis scripts (#433 scope-narrowing)

[turbomam]

Why

Scope-narrowing per #433: metpo/presentations/ holds one-off analysis / slide-generation scripts (BactoTraits, Madin, kg-microbe, ontology-landscape, SSSOM, ontogpt-grounding, etc.) that are not part of the ontology build, the released artifacts, or the production CLI surface. Removing them shrinks the maintenance footprint and the CodeQL/quality surface (one of these scripts was flagged in the recent scan).

Sibling to #441 (retire notebooks/).

What

• Removes the 8 metpo/presentations/*.py modules and the package __init__.py.
• Drops the now-unused presentations exclusion from ruff.toml.
• Updates README.md, docs/CLI_STANDARDIZATION_PLAN.md, docs/METPO_CAPABILITIES.md to reflect the removal.
• No [project.scripts] entry points or Makefile targets reference metpo.presentations, and nothing imports it, so nothing downstream breaks (verified; ruff + pytest green).

Branch is up to date with main.

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Retires the metpo/presentations/ directory as part of the scope-narrowing tracked in #433. These were one-shot analysis/figure-generation scripts for the ICBO 2025 talk, not part of the ontology build, released artifacts, or any CLI entry point. Removing them shrinks the maintenance and security-scanning surface; they remain recoverable from the 2025-11-17 release tag.

Changes:

• Delete all 8 metpo/presentations/*.py modules plus the package __init__.py.
• Drop the now-unused metpo/presentations/* per-file ignores from ruff.toml.
• Update README.md, docs/CLI_STANDARDIZATION_PLAN.md, and docs/METPO_CAPABILITIES.md to note the retirement and point to the recovery tag.

Reviewed changes

Copilot reviewed 13 out of 14 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
metpo/presentations/__init__.py	Removed (package retirement).
metpo/presentations/analyze_bactotraits.py	Removed one-shot ICBO analysis script.
metpo/presentations/analyze_kg_microbe_metpo.py	Removed one-shot ICBO analysis/figure script.
metpo/presentations/analyze_madin_etal.py	Removed one-shot ICBO analysis script.
metpo/presentations/analyze_ontogpt_grounding.py	Removed one-shot grounding-stats script.
metpo/presentations/analyze_ontology_landscape.py	Removed one-shot landscape-summary script.
metpo/presentations/analyze_primary_sources.py	Removed ChromaDB/SSSOM primary-source dump script.
metpo/presentations/analyze_sssom_mappings.py	Removed SSSOM-mapping summary script.
metpo/presentations/calculate_minimum_import_set.py	Removed import-set heuristic script.
metpo/presentations/generate_feedback_loop.py	Removed matplotlib slide-figure script.
ruff.toml	Dropped the now-dead per-file ignores for the deleted scripts.
README.md	Documents that the presentation scripts live at tag 2025-11-17 and how to recover them.
docs/CLI_STANDARDIZATION_PLAN.md	Marks Category 4 (presentation scripts) as retired.
docs/METPO_CAPABILITIES.md	Replaces the table of presentation scripts with a retirement note + recovery command.

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[turbomam]

Parking this as a draft. Per Mark: do not merge (i.e. do not delete presentations/) until the long-term destination for non-ontology content is decided. Retiring this code is part of finding it a better home, not just removing it. Will mark ready-for-review once that decision is made.