fix(statmech): declare reaction species in the Arkane kinetics input regardless of compute_thermo

[alongd]

What this fixes

An Arkane kinetics input generated by ARC can reference species it never declares, so Arkane dies before computing anything:

File "arkane/input.py", line 297, in reaction
    reactants = sorted([species_dict[spec] for spec in reactants])
KeyError: '[O]C=O[1]'

This was found on a run where everything else went right: two species and a transition state all optimised and frequency-checked on a cluster, and then no rate coefficient at all.

Cause

ArkaneAdapter.render_arkane_input_template builds species_list under if e0_only or spc.compute_thermo:. A caller that sets compute_thermo=False — as an orchestrator does when it wants kinetics but does not want a full thermodynamics job queued — gets:

• the E0 render (e0_only=True) → gate passes → all species declared;
• the kinetics render (e0_only=False) → gate fails → none declared, while reaction(...) still names them by label.

generate_species_files writes the per-species statmech files either way, so ARC writes statmech/kinetics/species/<label>.py to disk and then writes a main input that references that species without declaring it. compute_thermo should govern whether a thermo job runs — not whether a species may be declared in an input that names it.

The existing test_generate_arkane_input never caught this because ARCSpecies.compute_thermo defaults to not is_ts, i.e. True for ordinary species; the defect only surfaces when a caller sets it to False explicitly.

The change

Collect the labels named by any reaction in the render's reaction list, and let a species through the gate if it is one of them:

if e0_only or spc.compute_thermo or spc.label in reaction_species_labels:

Deliberately narrow rather than dropping the gate: dropping it would push species into thermo inputs that exclude them on purpose. For a thermo render self.reactions is None, so the new set is empty and the gate is unchanged — thermo inputs are unaffected.

Testing

• New unit test: a reactant with compute_thermo=False now renders as a species('R', ...) line in a kinetics input.
• Mutation: restoring the old gate turns it red, with the rendered text showing reaction(reactants=['R'], products=['P']) above zero species( lines.
• arc/statmech/: 50 passed.
• End to end on real converged output. Taking the failing run's own kinetics input and adding only the two species(...) declarations this fix emits, Arkane exits 0 and writes the rate coefficient it previously could not produce:

  kinetics(label = '[O]C=O(1) <=> O=[C]O(8)',
      kinetics = Arrhenius(A=(36.3562,'s^-1'), n=3.33173, Ea=(61.8336,'kJ/mol'),
                           T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')))
  

  No new quantum chemistry — the converged logs were already on disk. (Those numbers come from an RMG-Py checkout that is behind main in arkane/, so treat them as a plumbing result, not a physical one.)

Note for anyone running these tests: arc/statmech/ needs -n0. Under the default xdist config test_generate_arkane_input flakes, because sibling workers share the on-disk arc/testing/arkane_input_tests_delete directory. Pre-existing and unrelated to this change.

---

Separately: an unrelated bug found on the same run

arc/job/ssh.py:42-43 unpacked self.connect(), which returns None. Not fixed here, and no longer needs to be: @calvinp0 pointed out it is already fixed in #1001 (self._sftp, self._ssh = self.connect() → self.connect(), with a regression test). Tracked there.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 64.63%. Comparing base (735de21) to head (4fbafa6).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1022      +/-   ##
==========================================
+ Coverage   64.61%   64.63%   +0.01%     
==========================================
  Files         119      119              
  Lines       39830    39831       +1     
  Branches    10313    10312       -1     
==========================================
+ Hits        25736    25743       +7     
+ Misses      11116    11104      -12     
- Partials     2978     2984       +6     

Flag	Coverage Δ
functionaltests	64.63% <ø> (+0.01%)	⬆️
unittests	64.63% <ø> (+0.01%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

Fixes ARC-generated Arkane kinetics inputs that referenced reactant/product labels in reaction(...) blocks without declaring the corresponding species(...) entries when ARCSpecies.compute_thermo=False, which could cause Arkane to fail early with a KeyError and produce no kinetics output.

Changes:

• Ensure any species named by reactions is included in the Arkane input species_list regardless of compute_thermo (while preserving the existing gate for non-reaction species).
• Add a unit test covering kinetics-input rendering when reactants/products have compute_thermo=False.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
arc/statmech/arkane.py	Expands the species-declaration gate so kinetics renders always declare reaction participants, preventing Arkane KeyError on undeclared species labels.
arc/statmech/arkane_test.py	Adds regression test asserting reaction species are declared in kinetics inputs even when compute_thermo=False.

---

💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.

[calvinp0]

Separately: an unrelated bug found on the same run, reported not fixed here

arc/job/ssh.py:42-43 does

self._sftp, self._ssh = self.connect()

but connect() (arc/job/ssh.py:346-368) returns None, so this raises TypeError: cannot unpack non-sequence NoneType. It only bites a fresh SSHClient used outside a with block, which is why it has survived: there is exactly one production call site, arc/job/trsh.py:1488, on the troubleshoot-by-changing-node recovery path. Not touched here to keep this PR to one change — flagging it so it is not lost.

Should be fixed in #1001

[alongd]

You're right — checked #1001 and it fixes exactly this: self._sftp, self._ssh = self.connect() → self.connect(), with a regression test for it. Dropping the note from this PR's description so the fix is tracked in one place.