fix(pdep): let the pdep parser read T3's own transitionState('TS2', 'qm/TS2.py')

[alongd]

What this fixes

T3's PES exploration loop crashed in round 1 on a hybrid network file T3 itself wrote in round 0, during the first run of the loop against real quantum chemistry:

ValueError: The pdep network file at '.../round_0/hybrid/network0_reduced.py' calls
'transitionState(...)' with 2 POSITIONAL argument(s); refusing to parse it because this module
reads keywords by name and would silently record the positional values as absent.

t3/pdep/hybrid.py emits transitionState('TS2', 'qm/TS2.py') when it vendors a QM-adopted transition state; t3/pdep/parser.py::_call_keywords refuses every positional argument. Producer and consumer are both inside T3 and they disagreed.

Why the fix is on the reader's side

The obvious fix — make the writer use keywords — does not work. arkane/input.py:241 is def transitionState(label, *args, **kwargs), and its load-a-statmech-file-from-a-path branch is guarded by if len(args) == 1 and len(kwargs) == 0. Arkane offers no keyword spelling for path-loading, and Arkane reads this same file, so transitionState(label=..., path=...) would silently stop loading the QM statmech file.

The guard's premise is what was wrong. Its comment justifies refusing positionals by surveying "zero of the 156 parseable files under RMG-Py's examples/ and arkane/data/". That survey is real and its conclusion does not hold here, because the corpus never contained T3's own writer's output.

The change

One narrow exception in _call_keywords, ahead of the unchanged refusal: when the call is transitionState with exactly two positional arguments and no keywords, map args[0] -> label, args[1] -> path. Every other positional shape — one or three-plus positionals, positionals mixed with keywords, and this same two-positional shape for species/reaction — still falls through to the refusal, which is deliberate: mapping positions to names generally would mean duplicating Arkane's signatures and keeping them in step forever.

Both _call_keywords call sites that can see a transitionState node (parse_pdep_network_text and parse_pdep_network_e0_text) pass call_name and are therefore covered.

Testing

The real crashed artifact is vendored at tests/data/pdep_hybrid/positional_ts/network0_reduced.py with a provenance README, since the run directory it came from is scratch.

• It parses, and the parse recovers both the label and the path ({'label': 'TS2', 'path': 'qm/TS2.py'}) — not merely "no exception raised".
• Mutation: removing the exception turns those tests red with the verbatim production error; restoring it returns them to green.
• tests/test_pdep: 1902 passed.

Not covered, deliberately

arkane/input.py line ~130 gives species(label, *args, **kwargs) the identical path-loading shape, so the same trap is latent there. T3's writer never emits a positional species(...) — the hybrid writer's species channel is keyword-form — so covering it now would widen the guard to a spelling nothing writes, and would need a fabricated fixture. Until a writer path does emit it, the parser refuses loudly rather than mis-parsing silently, which is the safe failure direction.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.71%. Comparing base (3992f60) to head (92f10be).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #197      +/-   ##
==========================================
- Coverage   82.73%   82.71%   -0.02%     
==========================================
  Files          72       72              
  Lines       11720    11722       +2     
  Branches     2526     2527       +1     
==========================================
  Hits         9696     9696              
- Misses       1433     1434       +1     
- Partials      591      592       +1     

Flag	Coverage Δ
unittests	82.71% <ø> (-0.02%)	⬇️

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[Copilot]

Pull request overview

This PR fixes a producer/consumer mismatch within T3’s pdep hybrid workflow by teaching the pdep parser to accept Arkane’s required two-positional transitionState(label, path) form that T3 itself writes into hybrid network files.

Changes:

• Allow _call_keywords to map transitionState('TS2', 'qm/TS2.py') into {'label': ..., 'path': ...} while continuing to refuse other positional-argument shapes.
• Add regression tests asserting the real hybrid artifact parses and that both label and path are recovered.
• Vendor the real crashed hybrid network file plus provenance documentation under tests/data/.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
t3/pdep/parser.py	Adds a narrowly-scoped exception so transitionState(label, path) positional form is parsed into keywords.
tests/test_pdep/test_parser.py	Adds regression tests covering the real crashed artifact and the narrowness of the exception.
tests/data/pdep_hybrid/positional_ts/README.md	Documents provenance and the load-bearing line in the vendored artifact.
tests/data/pdep_hybrid/positional_ts/network0_reduced.py	Adds the byte-for-byte hybrid network fixture that previously triggered the crash.

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