Build a real deployed simulator definition on the container, and survey the associated repositories

[jcschaff]

Two things. test_build_simulator moves off cluster_only, and a read-only survey of the associated repositories is added.

1. The build test runs on the container

Leaves seven cluster-only tests. It builds a definition copied verbatim from the live deployment, so singularity build --fakeroot is exercised against content a deployment really produced rather than something a test invented. It asserts the image is produced and executes, not merely that the job exited zero.

The fixture is simulator version 34 from https://compose.cam.uchc.edu/core/simulator/list, saved with a README recording its provenance and how to refresh it. Of the 37 versions published there it is the smallest.

	this fixture	newest published definition
build time	~70s	minutes
image size	594 MB	1.3 GB
dependencies	one git package	copasi, tellurium, readdy, micromamba

The package introspection the old version did is dropped: it exercised pbest's default dependency set rather than the build, and tied the test to a pin that changes.

This one costs real CI time, and that is a decision for you

	before	after
CI per job	~2m	~6m20s
runner time per push	~8m	~25m

Four jobs, because CI still runs twice per push. It buys the first coverage anywhere of the fakeroot build path against real content. If that is too much, the cheapest lever is moving this single test to a scheduled job; the second cheapest is fixing the duplicate-CI trigger (finding F4).

Two hazards it surfaced

The formatter silently invalidated the fixture. Pre-commit's end-of-file-fixer appended a newline, changing its md5 and so its identity, turning a verbatim copy into something that merely resembled one. tests/fixtures/resources/ is excluded from the whitespace hooks now, and the test asserts the hash still equals the value the deployment recorded.

The same race as F13, in a new place. Asserting the recorded status immediately after the scheduler reports the job done depends on the monitor having polled. It now waits.

2. docs/ecosystem-repos.md

Read-only survey, checked against GitHub and PyPI on 2026-09-12. Nothing was changed in any other repository.

bsew and bsander live in biosimulators, not vivarium-collective. Neither is on PyPI; both return 404. Neither was documented here, and both already reach this repository. The sharper finding: bsew is installed into a deployed simulator image by a bare git clone with no branch, tag or commit, so the image depends on whatever main is at build time. That is item 6 of the runtime plan, concrete and in production rather than hypothetical. bsander reaches us only through the dead uv.sources override already recorded as F14. Both are load-bearing in the grant narrative while being unreleased and idle for nine and twelve months.

The wrappers are no longer called pbg-. The organisation completed a pbg- to viva- rename: 54 viva- repositories against a single surviving pbg-. Anything still looking for pbg-xxx finds almost nothing.

An index already exists, generated nightly by viva-catalog from a GitHub topic, so the document deliberately does not restate the list — a second hand-maintained index would be stale in weeks. It records how to read that index and where it does not reach: 7 repositories are absent, all tooling rather than simulator content, so it answers "what can I compose with" rather than "what does this ecosystem consist of".

The consolidation question is framed, not answered. Evidence points away from the wrappers, which have separate upstreams and cadences and are already addressable, and toward the tooling layer: three paths delegate to process_bigraph.Composite, four partial static checkers exist, and three ways to containerise a composite. Four questions are listed for a decision that is not mine to make.

Verification

• CI green on 3.13 and 3.14, both duplicate runs.
• Locally: 40 passed, 7 skipped, 279s.
• The built image runs: Python 3.12 with bsew importable inside it.
• The fixture's hash matches what the deployment recorded, and survives make check.

🤖 Generated with Claude Code

https://claude.ai/code/session_018TgVbCXXWAWhNjtKTzrxvN