merge: rename the limma probe out of pytest's collection path

docs/adr/ADR-0007-phase1-local-validation.md

@@ -21,7 +21,7 @@ bridge's real streamable-http handshake was implemented (was a mock-only stub).
 - [x] `pytest tests/test_sandbox_executor.py tests/test_executor_seam.py` →
       **27/27** (was 22; +5 regression tests added for the fixes below).
 - ⚠ A single-invocation `pytest -q` **cannot collect** the whole repo: (a)
-  `scripts/test_limma_runtime.py` is a standalone script that `sys.exit(1)`s at
+  `scripts/check_limma_runtime.py` is a standalone script that `sys.exit(1)`s at
   import when rpy2 is absent, and (b) the `tests/` files insert `sys.path`
   differently, so collecting them together pollutes `managers` import resolution.
   **Both are pre-existing and unrelated to this branch** (confirmed: not in the

pytest.ini

@@ -1,11 +1,11 @@
 [pytest]
-# Bare `pytest` from the repo root used to die with an INTERNALERROR before
-# running a single test: pytest collects any `test_*.py`, and
-# scripts/test_limma_runtime.py is a standalone rpy2/limma diagnostic that calls
-# sys.exit(1) at import when rpy2 is absent — which aborts collection outright.
-# It is named test_* because it is run by hand (`python scripts/test_limma_runtime.py`),
-# not because it is a pytest module.
+# Belt-and-braces. The actual fix was renaming the offender:
+# scripts/test_limma_runtime.py -> scripts/check_limma_runtime.py. It is a
+# hand-run rpy2/limma diagnostic that calls sys.exit(1) at import when rpy2 is
+# absent, and pytest collected it on the test_* filename alone — which aborted
+# the whole run with an INTERNALERROR before a single test executed.
 #
-# testpaths applies only when no path argument is given, so `pytest` and
-# `pytest tests/` now agree, and `pytest scripts/...` still works if wanted.
+# testpaths keeps that from recurring if another test_*.py is ever dropped into
+# scripts/ or elsewhere outside tests/. It applies only when no path argument is
+# given, so `pytest` and `pytest tests/` agree, and an explicit path still works.
 testpaths = tests

scripts/{test_limma_runtime.py → check_limma_runtime.py}

@@ -3,7 +3,7 @@ Runtime test: verify the rpy2-limma bridge is functional.
 
 Run this in the Space terminal or locally after installing R and rpy2:
 
-    python scripts/test_limma_runtime.py
+    python scripts/check_limma_runtime.py
 
 Expected output:
     R version: R version 4.x.x (...)