Skip to content

Fix per stage ABFE BAR_Error by using correct loop var - #456

Merged
orbeckst merged 4 commits into
alchemistry:masterfrom
jberg5:fix-per-stage-bar-error
Jun 1, 2026
Merged

Fix per stage ABFE BAR_Error by using correct loop var#456
orbeckst merged 4 commits into
alchemistry:masterfrom
jberg5:fix-per-stage-bar-error

Conversation

@jberg5

@jberg5 jberg5 commented Apr 19, 2026

Copy link
Copy Markdown
Contributor

Fixes #455.

Also updated the example docstring with corrected per-stage error values.

@jberg5

jberg5 commented Apr 19, 2026

Copy link
Copy Markdown
Contributor Author

CI failure is

Run ruff format --check .
Would reformat: src/alchemlyb/parsing/lammps.py

Think that's outside the scope of this PR. Happy to format if you'd like though.

@codecov

codecov Bot commented Apr 19, 2026

Copy link
Copy Markdown

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.01%. Comparing base (220141f) to head (d6d451c).

Additional details and impacted files
@@           Coverage Diff           @@
##           master     #456   +/-   ##
=======================================
  Coverage   99.01%   99.01%           
=======================================
  Files          29       29           
  Lines        2446     2446           
  Branches      464      464           
=======================================
  Hits         2422     2422           
  Misses          2        2           
  Partials       22       22           

☔ View full report in Codecov by Sentry.
📢 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.

@jberg5

jberg5 commented Apr 19, 2026

Copy link
Copy Markdown
Contributor Author

Test failure also seems unrelated:

FAILED src/alchemlyb/tests/parsing/test_lammps.py::test_u_nk - assert (78682, 16) == (78681, 16)

@orbeckst

Copy link
Copy Markdown
Member

I raised #458 for the failures that seem unrelated to your changes.

For the ruff formatting a separate PR with only formatting changes would be preferred.

I'll merge the PR given that @xiki-tempula approved it.

@orbeckst orbeckst left a comment

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for the fix. Please

  • add yourself to AUTHORS under a new 2026 heading
  • add your GitHub handle to the 2.6.0 author line in CHANGELOG

Happy to merge then.

@jberg5

jberg5 commented Jun 1, 2026

Copy link
Copy Markdown
Contributor Author

Thanks @xiki-tempula and @orbeckst ! Have made the requested changes. Should I add myself to CITATION.cff as well? (AUTHORS recommends it, but want to double check with you folks)

@orbeckst

orbeckst commented Jun 1, 2026

Copy link
Copy Markdown
Member

Yes, please, add yourself after

alchemlyb/CITATION.cff

Lines 109 to 112 in 220141f

- given-names: Jennifer A.
family-names: Clark
orcid: https://orcid.org/0000-0003-4897-5651
affiliation: National Institute of Standards and Technology

Good point!

@orbeckst orbeckst left a comment

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Add yourself to CITATION.

I'll fix CHANGELOG.

I'll approve, assuming that the CITATION.cff fix will happen before anyone merges.

Comment thread CHANGES Outdated
@jberg5

jberg5 commented Jun 1, 2026

Copy link
Copy Markdown
Contributor Author

Ah nice, thanks for the fix. Have updated citation.cff

@orbeckst
orbeckst merged commit 5c029f5 into alchemistry:master Jun 1, 2026
11 of 13 checks passed
@orbeckst

orbeckst commented Jun 1, 2026

Copy link
Copy Markdown
Member

Thank you @jberg5 , much appreciated!!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

ABFE generate_result() gives incorrect BAR_Error

3 participants