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Package Map

The repository exposes three package roles. They are related, but they are not three equivalent public products.

bijux-phylogenetics is the public center of gravity. phylogenetic is the shorter compatibility install surface. bijux-phylogenetics-dev is repository-owned maintainer tooling.

flowchart LR
    A[bijux-phylogenetics] --> B[Canonical runtime]
    C[phylogenetic] --> A
    D[bijux-phylogenetics-dev] --> E[Docs, release, quality stewardship]

Package Roles

Package Role When to use it When not to use it
bijux-phylogenetics Canonical runtime package Normal runtime use, public docs, canonical CLI and Python surface Not when you only need maintainer tooling
phylogenetic Compatibility alias package You need the shorter distribution and CLI name with the same runtime story Not as a separate capability or documentation surface
bijux-phylogenetics-dev Maintainer tooling package Docs checks, release support, repository quality tooling Not as an end-user scientific runtime

What Each Package Signals Publicly

  • bijux-phylogenetics signals the full runtime identity, the full public documentation story, and the canonical CLI and Python imports
  • phylogenetic signals compatibility and convenience, not a distinct product line
  • bijux-phylogenetics-dev signals repository stewardship, not scientific runtime consumption

Choice Rule

  • Install bijux-phylogenetics for normal product use.
  • Install phylogenetic only when the shorter compatibility name is the real requirement.
  • Use bijux-phylogenetics-dev only when maintaining this repository.

That split keeps the public story stable instead of letting package names drift into overlapping meanings.