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Establish scientific model library and developer workflow - #1

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PraneethMerugu merged 1 commit into
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codex/model-library
Sep 8, 2026
Merged

PraneethMerugu merged 1 commit into
mainfrom
codex/model-library

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Scientific model library and developer workflow

R01 of the ecosystem delivery map. Establish PottsModels as the owner of
complete model factories and tutorials, using public Potts APIs rather than a
second executor. The companion Potts PR removes the displaced full examples.

Included

  • Bounded Wortel, Merks, and OpenVT-inspired factories, initializers, returned
    scientific references, and documented modeling assumptions.
  • Three executable tutorials, ordinary model and package-quality tests, and
    explicit developer/test/documentation environments.
  • Hosted CI selecting explicit ecosystem revisions without mutating runtime
    dependencies or requiring Potts/Core to depend on PottsModels.

Local validation

  • Complete ordinary package suite: 65 assertions passed.
  • Independent comparison with the original examples: 12 saved-trajectory and
    channel assertions passed.
  • Strict documentation build and all three tutorials passed.
  • Workflow syntax and candidate dependency selection were independently reviewed.

Hosted CI is a separate required validation of this PR and has not been inferred
from those local results. The persistent-task Aqua check has a documented
exclusion because its fresh environment cannot resolve unregistered developed
dependencies; ordinary environment loading and precompilation were exercised.

Scope

These factories demonstrate bounded sequential-CPU models, not calibrated paper
reproductions or newly established GPU guarantees. The OpenVT-inspired example
does not establish a growing contact-inhibited tissue law. Broader models,
authoring features, and device combinations remain later work in the chain.

@PraneethMerugu
PraneethMerugu merged commit 4f259dc into main Sep 8, 2026
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