[Jammy2211]

Summary

Closes #227.

Heart check F is the release-time "Colab simulation", and until now it emulated Colab by pip install autolens jax with dependencies. That venv already held every package the real --no-deps bootstrap in autonerves.setup_colab would miss, so the check could never see a missing dependency. On 2026-09-15 corner — a base autofit dependency imported lazily inside corner_cornerpy — was absent on Colab and HowToFit tutorial 5 died mid-workshop after its emcee run; workspace smoke (PYAUTO_TEST_MODE=2, samplers never constructed) and check F both reported green.

This PR makes check F a faithful Colab gate:

• Ground truth instead of an approximation. The sim venv (python3.12, Colab's interpreter) is seeded from Google's published Colab manifest (googlecolab/backend-info pip-freeze.txt, fetched live → $HEART_STATE_DIR cache → vendored snapshot), installing only the manifest packages the stack's resolved closure needs, completed to a self-consistent subset. Nothing absent from Colab's manifest is ever installed.
• The real bootstrap. The injected setup cell runs verbatim (pip install autonerves --no-deps → setup_colab.setup("autolens") → workspace clone), unchanged.
• Prove what the libraries import. After the bootstrap, the gate walks every declared requirement of the installed PyAuto packages, AST-scans them for every third-party import at any depth (recording whether the site is guarded by a try/except ImportError), imports each module for real, and constructs af.Emcee/DynestyStatic/Nautilus/LBFGS. Unguarded import failure → FAIL (readiness RED, stage-3 report fails). Guarded misses, version conflicts and never-imported declared deps → WARN.
• Scoping decision recorded on the issue: this is rung 2 of the prompt's ladder (~70 s, in the existing release-only verify_install_release lane); running notebooks end to end at real settings (rungs 3/4) tests a different bug class and is declined for this gate.

Witness (both legs run locally against live PyPI, manifest fetched live 2026-09-15)

Leg	Setup	Result	Wall
1	PyPI as-is	F FAIL colab gate: blackjax (…/blackjax/nuts/search.py:260); colossus (autolens/lens/los.py:207); corner (autofit/non_linear/plot/samples_plotters.py:95); +6 more	74 s
2	COLAB_GATE_AUTONERVES_SRC = PyAutoNerves feature/colab-bootstrap-lazy-deps (PyAutoNerves#167)	F FAIL colab gate: colossus (autolens/lens/los.py:207); hmf (autolens/lens/los.py:147); jax_zero_contour (autogalaxy/operate/lens_calc.py:1452); +3 more	66 s

Leg 1 reproduces the 2026-09-15 failure that every existing gate missed. Leg 2 shows the gate flips on exactly the _SHARED_EXTRAS change: PyAutoNerves#167 clears corner and blackjax and five of seven version conflicts.

Merge consequence and how the holes were closed

The gate found five library-side unguarded lazy imports of packages Colab does not ship. They were resolved on 2026-09-15, in two places:

• Real Colab breakages → _SHARED_EXTRAS on the PyAutoNerves branch (PyAutoNerves#167 follow-up PR): jax_zero_contour>=2.0.0,<3.0.0 (an autogalaxy base dependency reached by autogalaxy/operate/lens_calc.py:1452,1884, guarded at plot_utils.py:429 but not there) and zeus-mcmc==2.5.4 (af.Zeus, run by autofit_workspace notebooks). Every runtime requirement of both is already shipped by Colab.
• Not notebook paths → heart/config/colab_gate.yaml accepted_missing, each with a written reason (second commit on this PR): colossus and hmf (autolens/lens/los.py line-of-sight tooling, test/dev extra; hmf is declared in no pyproject at all, a library follow-up), and mcp (autofit/mcp/server.py, the MCP server entry point, unconditional import is correct there).

Leg 3 (this PR + the extended Nerves branch overlaid):

F      PASS    Colab manifest live 2026-09-15; 87 Colab-provided, 11 extras, 39 imports probed

179 s, 0 FAILs, 32 WARNs (the three accepted names with reasons echoed; networkx==3.1 / psutil==6.1.0 autofit pins vs Colab 3.6.1 / 5.9.5; guarded coolest, nufftax; five declared-but-never-imported deps; the 20 closure packages Colab does not ship, all now arriving via extras).

The release-integrate run stays RED until the autonerves carrying PyAutoNerves#167 and its follow-up is on PyPI — check F installs autonerves from the index. That is the gate working; the ordering is: merge this, merge the Nerves PR, release autonerves.

Scripts Changed

• heart/checks/colab_gate.py (new) — seed / verify gate. seed resolves the with-deps closure via pip install --dry-run --report - without installing it, installs only the part Colab also ships at Colab's pins, then completes that set to a self-consistent Colab subset. verify walks declared requirements, AST-scans every import (guarded = inside a try whose handlers catch ImportError/ModuleNotFoundError/Exception/bare), probes each module for real (a failing module whose distribution Colab ships is installed at Colab's pin and re-probed), constructs the four tutorial searches, and applies the verdict. Stdlib + packaging; pure functions throughout; JSON report.
• heart/checks/colab_pip_freeze.snapshot.txt (new) — vendored googlecolab/backend-info manifest, fetched 2026-09-15; last fallback behind live fetch → $HEART_STATE_DIR/colab_pip_freeze.txt cache.
• heart/config/colab_gate.yaml (new) — accepted_missing: exemptions keyed by module name, each with a one-line reason: colossus, hmf, mcp (see above). A shipped-config test asserts exactly this set.
• heart/checks/verify_install.sh — check F rebuilt: python3.12 venv (missing interpreter → FAIL, the check B/E rule), the with-deps pip install <stack> jax deleted, gate seed before the setup cell and verify between the setup cell and the notebook cell. Setup cell, google.colab stub, exit-3 SKIP and the cosmos_web_ring notebook cell unchanged. New COLAB_GATE_AUTONERVES_SRC dev/witness overlay. Gate JSON nested additively at checks[F].colab_gate in the readiness sidecar; gate temp files swept via ARTEFACTS (honours --keep).
• tests/test_colab_gate.py (new, 34 tests) + tests/test_verify_install_script.py (+9) — manifest parsing/normalisation, live→cache→snapshot fallback, closure intersection, requirement walk, AST scan, verdict rules incl. accepted_missing and the imported-missing FAIL, and a round-trip of the real sidecar writer through readiness.compute. No network, no venv.
• skills/verify_install/verify_install.md, docs/release_validation.md, health_agent/capabilities.yaml, bin/pyauto-heart — check F description rewritten (the old row still named autoconf and dataset/imaging/simple), with an explicit statement of what the simulation does not cover: GPU, OS, and the manifest's 1–2 day lag.

Test Plan

• python3 -m pytest -q -n auto in PyAutoHeart: 1015 passed (baseline 1013 + the new modules' own tests; the two late fixes — seed completion and import heal — brought their own tests)
• Witness leg 1: check F against PyPI → F|FAIL naming corner (74 s)
• Witness leg 2: PyAutoNerves#167 branch overlaid → corner, blackjax cleared; five library-side FAILs remain (66 s)
• Sidecar with nested colab_gate parses through readiness.compute
• Witness leg 3: this PR + extended Nerves branch → F|PASS (179 s), 1016 tests
• Human: release autonerves after both PRs merge (check F installs it from the index)

Generated by the PyAutoLabs agent workflow.

🤖 Generated with Claude Code

[Jammy2211]

Leg 3: with the extended PyAutoNerves branch (jax_zero_contour + zeus-mcmc in _SHARED_EXTRAS; colossus/hmf/mcp accepted with reasons in colab_gate.yaml) check F reports F|PASS in 179 s — 87 Colab-provided, 11 extras, 39 imports probed, 0 FAILs / 32 WARNs. 1016 unit tests green.

[Jammy2211]

Nerves PR: PyAutoLabs/PyAutoNerves#169