[jonas-fuchs]

This is aimed to improve how phenotypes are displayed/accepted. The idea is to better reflect individual databases.

New features:

• Rank-based phenotype severity vocabulary (phenotype_ranks.py) with five tiers plus unknown/contradictory sentinels, shared across import, algorithms, and reporting; threshold keys accept bare ranks (1–5) or labels.
• Maintained-database version compatibility check: manifests can require respro >=X.Y.Z, failing --list/--download fast on incompatible installs.
• Web: hosted chemical-structure and feature-sequence viewers in the Analyze tab, with a parent-owned DNA/Protein toggle; frontend rank vocabulary in utils.js mirroring the Python source.

Bug fixes:

• regenerate now reconstructs profiled features per reference (from JSON or the new profiled_feature results-DB table) so susceptible drugs appear in the summary table.
• Contradictory phenotype resolution corrected: it now sits between susceptible (rank 1) and rank 2, winning over susceptible/unknown but losing to higher tiers.

Improvements:

• Removed ic50_thresholds algorithm from import, algorithms, reporting, and the web database browser.
• Report summary narrative lists only non-zero categories using rank terminology and colours lines by rank.
• Web DatabaseTab renders one severity-ordered column per configured phenotype label.
• Documentation overhaul reflecting the rank vocabulary and removed algorithm.

Breaking changes:

• ic50_thresholds removed; databases/configs referencing it must migrate to drug_interpretation.
• Phenotype labels constrained to the rank vocabulary; unrecognized labels map to unknown.
• Package version bumped to 0.2.0; frontend requires React 19 / Vite 8 / Vitest 5 / Plotly 4.

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