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Repair dev/integration_tests: PythonCall fails to initialize (pixi/NFS); silent skip reads as pass #52

@kalidke

Description

@kalidke

While gating the 0.5.0 release, the Python-SDK integration harness (dev/integration_tests/) would not run on kitt:

  1. Tracked Manifest.toml was stale — fixed: the manifest was resolved against another machine's depot and broke using PythonCall with could not find source path for package MbedTLS_jll. Now untracked/gitignored; each machine resolves its own.
  2. PythonCall still fails to initialize (during initialization of module C, UndefRefError from the Python dep setup) even after a fresh resolve. CondaPkg gets as far as Initialising pixi, then init dies — likely pixi env creation on the NFS $HOME. Needs investigation (options: JULIA_CONDAPKG_BACKEND=Null + system python with pip install -r requirements.txt, a non-NFS CONDA_PKG/pixi cache dir, or dropping PythonCall in favor of shelling out to python3 directly — the tests mostly orchestrate subprocesses anyway).
  3. Silent-skip default: runtests.jl skips the Python tests unless RUN_PYTHON_INTEGRATION_TESTS=true, and the skip run exits 0 with a green summary (External Integration Tests | 4 4) — easy to misread as the full gate passing. Consider printing a loud SKIPPED banner or failing when the env var is unset and the SDK is unavailable.

Not a 0.5.0 blocker: nothing in 0.5.0 touches this harness, and cross-client validation is covered by the e2e suite (real subprocess servers, 543/543) plus the MCP Inspector CI (external Node client) on every PR. But it should work before the next protocol-level release.

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