fix(outputs.py): handle missing trailing newline in ICOHPLIST.lobster #4350
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LOBSTER 5.1.1 sometimes produces an ICOHPLIST.lobster file without a trailing
newline, which causes the Icohplist parser to miscount bond entries (e.g., 1079 vs. 1080).
This commit updates the file-reading logic in Icohplist.__init__ to use splitlines()
and filters out any blank lines, ensuring that only valid, non-empty lines are parsed.
This change prevents the ValueError ("COHPCAR and ICOHPLIST do not fit together")
and aligns the bond count with COHPCAR.lobster.
Ref: See related issue in lobsterpy (materialsproject#389) for additional context.
Signed-off-by: Ali Hussain Umar Bhatti <[email protected]>
Contributor
|
Thanks, @alibh95, for raising this fix. Can you please also adapt the failing test in the PR? |
Member
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Please provide a unittest to check for this issue. Thanks. |
Contributor
|
Hi @alibh95 , it would be great if you can fix the newly added test that is failing and also adapt the existing failing test to reflect correct number of bonds |
- Strip only trailing blank lines so a missing final newline still works - Compute header length dynamically (skip title and optional spin‐line) - Determine LOBSTER version by column count (6→2.2.1, 8→3.1.1, 9→5.1.0) - Preserve non‐orbitalwise LCFO entries (fixes length mismatch for non-orbitalwise LCFO lists)
Contributor
Author
|
@shyuep I have added the unittest for this issue. |
Member
|
Thanks! |
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LOBSTER 5.1.1 sometimes produces an ICOHPLIST.lobster file without a trailing newline, which causes the Icohplist parser to miscount bond entries (e.g., 1079 vs. 1080). This commit updates the file-reading logic in Icohplist.init to use splitlines() and filters out any blank lines, ensuring that only valid, non-empty lines are parsed. This change prevents the ValueError ("COHPCAR and ICOHPLIST do not fit together") and aligns the bond count with COHPCAR.lobster.
Ref: #4349 and JaGeo/LobsterPy#389
Summary
Major changes:
Checklist
ruff.mypy.duecredit@due.dcitedecorators to reference relevant papers by DOI (example)Tip: Install
pre-commithooks to auto-check types and linting before every commit: