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Only process - #653
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #653 +/- ##
==========================================
- Coverage 67.18% 67.10% -0.08%
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Files 123 123
Lines 43674 43694 +20
Branches 11153 11160 +7
==========================================
- Hits 29342 29323 -19
- Misses 11194 11225 +31
- Partials 3138 3146 +8
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Pull Request Overview
This PR introduces an "only process" mode to ARC, allowing users to skip job spawning and only process existing calculations when restarting. The implementation adds an only_process parameter to control whether new jobs should be spawned, and improves species handling by preserving user-provided adjacency lists for better accuracy with complex nitrogen and sulfur species.
- Adds
only_processparameter to ARC and Scheduler classes to control job spawning behavior - Preserves user-provided adjacency lists in species definitions for better molecular representation
- Updates test cases to include
arkane_fileattribute in expected output dictionaries
Reviewed Changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| arc/scheduler.py | Adds only_process parameter to Scheduler class and prevents job spawning when enabled |
| arc/main.py | Adds only_process parameter to ARC class and passes it to Scheduler |
| arc/reaction/reaction_test.py | Updates test expectations to include arkane_file attribute in species dictionaries |
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…rift (#1066) ## What Adds a `codecov.yml` (23 lines, no code change): - `coverage.status.project.default.threshold: 1%` - `coverage.status.patch.default.target: 80%` ## Why ARC has no Codecov configuration at all — `.coveragerc` configures coverage.py's *collection*, not Codecov's *status checks*. With no config, Codecov falls back to its built-in defaults, under which the `project` status is `target: auto` with a **0% threshold**: total coverage may never dip by any amount relative to the base commit. The consequence is that nearly every PR adding code covered below the repository average (~67%) reports a failing check while every test job, CodeQL and the functional suite are green. Observed on the current open set, all red on `codecov/project` alone: | PR | status | |---|---| | #653 | `67.03% (-0.10%)` → `67.05% (-0.08%)` after adding a genuine unit test | | #860, #1016, #1039, #1050, #1054, #1055, #1056, #1057 | red on `codecov/project`, everything else green | On #653, `codecov/patch` simultaneously reported *"Coverage not affected"* — the gate that actually judges whether the PR's new code is tested was already satisfied. A check that fails on one-tenth of a percentage point trains reviewers to ignore it, which costs us the patch signal too. ## What this does and does not change - **Does:** lets total coverage drift up to 1% without failing the status. - **Does:** keep an explicit `patch` target, so the coverage of a PR's own new or changed lines remains a gating signal. This is the stricter half of the config, not a loosening. - **Does not:** touch any test or source file, change `.coveragerc`, or alter what coverage is collected. - **Does not:** raise ARC's actual coverage. That is a separate and much larger piece of work. Note that Codecov re-evaluates statuses on new uploads, so already-open PRs will pick this up on their next CI run rather than retroactively.
only_process was added with no test exercising it. Covers the arc/main.py side: stored on the instance, written to the restart dict only when truthy (so existing restart files are unchanged), and accepted back as an input key. Also covers the two paths a Copilot review found unguarded: - processing-only mode must not calculate a missing frequencies scaling factor. determine_scaling_factors() builds a Scheduler of its own that never sees only_process, and it is reached from ARC.__init__, so it would submit calibration jobs for small species before execute() ever reaches the guarded project scheduler. The test asserts it is not called, and asserts the same input without only_process does call it, so the guard is what stops it. - a monoatomic species' restored sp job must still be tracked after a restart. Its job_dict entry suppresses a replacement, so an un-tracked job leaves the species unconverged for the rest of the run. The schedule_jobs() guard itself stays uncovered: testing=True already short-circuits it.
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We'd like ARC to immediately process thermo/kinetics after all relevant jobs have ended.
This PR takes us one small step closer to this goal, adding an
only_processarg to the input (restart) file, to request ARC to only process what it can and not spawn new jobs in this restart mode whenonly_processisTrue.Also, save the species adjlist if given. Some species are not read correctly in RMG (especially hyperventilate N and S containing species), which results in excluding them from the final thermo library. Here we use the user-provided adjlist (which is the best way to define these species) if given.