stfc / aiida-feff

85%

Build Type

push

github

Committed by Kane Shenton

Commit Message

Fix provenance tracking, batch execution, and physics calculations

Comprehensive overhaul addressing calculation reproducibility, provenance
immutability, batch execution failures, and physical consistency across
the plugin.

Major changes:
- Provenance & metadata: Add versions module to track FEFF, pymatgen,
  and larch code versions. Move run metadata (E0, Fourier parameters,
  snapshot counts) from mutable extras to node attributes.
- CalcJob validation: Replace prepare_for_submission ExitCode returns
  with input spec validators on FeffCalculation and FeffBatchCalculation.
- Input parameter validation: Restrict FeffParameters, compute_msrd,
  compute_adp, and FT parameters to known keys with alias suggestions.
- EXAFS & FT consolidation: Move EXAFS equation to calcfunctions/exafs.py
  (verified against larch FeffPathGroup); unify Fourier transforms
  under xftf_arrays.
- Batch execution fixes: Fix dynamic output harvesting key matching
  (__ vs .); parse worker counts from resource options; support wallclock
  timeouts and compound string formats ("32(x2)").
- Geometry & path fixes: Ensure 3-body path closure using vector
  differences rather than uncoordinated minimum image conventions;
  make compute_msrd raise on unsafe MIC cutoffs (with allow_unsafe_cutoff
  override).
- Workflow & parser hardening: Distinguish potentials-only runs from
  crashed executions via CONTROL card checks; fix frame ordering past
  9999 frames; require explicit cells in trajectory_to_structures.
- Tests & CI: Add analytic limit tests (disorder, ADP, perpendicular
  bias) and full in-process ensemble integration tests. Wire pre-commit
  and uv-based mypy into CI.

BREAKING CHANGE: compute_msrd now raises a ValueError on unsafe minimum
image convention cutoffs instead of issuing a warning. Use
allow_unsafe_cutoff=True to bypass.

Coverage Stats

552 of 626 new or added lines in 20 files covered. (88.18%)

6 existing lines in 5 files now uncovered.

1903 of 2249 relevant lines covered (84.62%)

0.85 hits per line