[jcschaff]

Part 7c-4 of docs/plan-environment-composition.md. It is the last piece before 7c-5, the live run.

Changes

• New entries (all kind: library):
  • smoldyn-vcell: the OPTION_VCELL wheel from virtualcell/Smoldyn's release vcell-pyhybrid-e86d552, built by its workflow (ci: build the OPTION_VCELL Python wheel for compose-api, and release it virtualcell/Smoldyn#1, 7c-3). It installs by URL and sha256 bb033bcc…, which I checked on download.
  • vcell-fenics (git 4dab281), pyvcell-fvsolver 0.11.1, zarr 3.4.1.
• viva-pde-particle becomes composable:
  • install: git 21dfe46, fix(ensemble): one Process class per trial function, nothing imported from config vivarium-collective/viva-pde-particle#67's merge, with the reference extra;
  • its conda engines (fenics-dolfinx 0.10, MPICH, gmsh, netgen, VTK…);
  • requires for the libraries above, plus pyvcell and libvcell.
  • Its prebuilt image stays (D7c.3).
• members_of for a prebuilt image now includes its bundled entries' requirements, which the image installs its own way. Without this, a document of viva-pde-particle's classes alone would no longer be covered by its image and would make a mash-up. The tests caught it.
• Compliance case viva-pde-particle/fokker-planck-ensemble: its own example, four seeded PDE + Smoldyn trials, with the emitter fully qualified (D7c.2), and the seeded results as exact expectations. To support it, a scalar expectation's field may now be a path (values.2.0).
• One behaviour change: when viva-pde-particle's image isn't offered, a document of its classes now needs a mash-up. Only a signed-in caller may cause one, so an anonymous caller gets 401 ("sign in to have one made for this run") instead of a 400 saying the classes aren't installed.

Checked with compose-api's own code, in Docker (linux/amd64, the pinned pixi image), for a document of FokkerPlanckEnsemble + CopasiUTCStep + RAMEmitter (rerun at 21dfe46):

1. needed_entries gives ten entries; no declared environment covers them; composable agrees, so the service would make mash-05956395cf.
2. The generated pixi.toml locked in 45 s (462 packages).
3. The definition's URL check (_url_checks, from 7c-2) passed against the release.
4. pixi install --frozen succeeded.
5. compose-api's runner ran both cases, and its evaluator passed both: viva-pde-particle's nine expectations, and pbsim-common's COPASI case against its reference CSV.
6. find_violations admits the case document in the mash-up.

Tests: the case and the scalar path, the mash-up admitting all three classes, and the prebuilt image still chosen for viva-pde-particle's classes alone. make check passes. The full suite has only the 3 known order-dependent local failures.

EnsembleRunner (decided): it imported whatever its trial: "module:function" config named. viva-pde-particle#67 replaced it with one Ensemble class per trial function, so the case document names local:viva_pde_particle.ensemble.FokkerPlanckEnsemble and its config has no trial. The expected values are unchanged. The prebuilt image moves to the same commit as viva-pde-particle@2, an admin registration rather than a code change.

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