Update for openfe v1.9 by IAlibay · Pull Request #190 · OpenFreeEnergy/pontibus

IAlibay · 2026-03-07T15:54:49Z

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IAlibay · 2026-03-07T15:57:03Z

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codecov · 2026-03-07T16:30:55Z

Codecov Report

❌ Patch coverage is 92.88390% with 19 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.55%. Comparing base (4353fcb) to head (2e00013).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
...bus/tests/protocols/relative/test_protocol_slow.py	5.88%	16 Missing ⚠️
.../pontibus/protocols/relative/hybridtop_protocol.py	96.29%	1 Missing ⚠️
src/pontibus/protocols/relative/hybridtop_units.py	97.50%	1 Missing ⚠️
...bus/tests/protocols/solvation/test_tokenization.py	98.36%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #190      +/-   ##
==========================================
- Coverage   96.10%   93.55%   -2.56%     
==========================================
  Files          35       38       +3     
  Lines        3263     3195      -68     
==========================================
- Hits         3136     2989     -147     
- Misses        127      206      +79

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IAlibay · 2026-03-08T08:41:27Z

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IAlibay · 2026-03-08T20:23:39Z

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IAlibay · 2026-03-08T20:24:55Z

The code has now all been updated and works for v1.9.
All that remains is docs, but that is blocked until #189 is complete.

… update-ci

j-wags

This looks great! Neither of my comments requests changes, just notes. This should be good to merge once #178 is merged in and tests pass!

j-wags · 2026-03-17T17:35:27Z

+          this solvent component.  Default `False`
        ion_concentration : openff.units.Quantity, optional
-          ionic concentration required, default 0.15 * unit.molar
+          ionic concentration required, default 0.0 * unit.molar
          this must be supplied with units, e.g. "1.5 * unit.molar"


👍 Good catch!

Added docstring to test classes explaining protocol results generation and simulation duration.

Added docstring to clarify protocol result generation and simulation expectations.

IAlibay · 2026-03-17T18:46:52Z

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j-wags

Ah, my apologies - In my review and in our meeting earlier this week, I'd said:

This should be good to merge once #178 is merged in and tests pass!

I had misunderstood and thought that this PR couldn't run the slow/GPU tests on AWS without #178, but I now see that AWS tests haven't been run because they need to be manually dispatched (and since they're billed to OpenFE I'm not comfortable dispatching them myself). So I no longer think #178 is a blocker for this PR to be merged.

That said, it WOULD be good to run the AWS GPU and CPU tests on this branch but since I've already misspoken once on this topic I'm not going to call this a blocker. Sorry for the confusion, I'd be happy to discuss this synchronously in our meeting next week to ensure I'm not misunderstanding yet again.

IAlibay · 2026-03-19T17:35:13Z

I'm a little bit lost 😅 - can I suggest we don't merge this PR until we discuss it next week?

j-wags · 2026-03-19T17:36:50Z

Absolutely, I've added this to our meeting agenda. Apologies again for the confusion.

Add runners for main branch deps

…-v1.9

IAlibay · 2026-03-24T17:48:32Z

@@ -0,0 +1,68 @@
+name: "CI - main branch of deps"
+on:
+  pull_request:


@atravitz not sure if it was intention for this not to be triggered on PR. From discussions today, it sounds like that behaviour we wanted, so I added it. However I'm happy to remove it.

Opened #192 so that we can decouple it from this PR and revisit it later.

IAlibay · 2026-03-24T20:03:15Z

GPU tests pass locally.

IAlibay · 2026-03-24T21:36:09Z

CPU vslow tests running here: https://github.com/OpenFreeEnergy/pontibus/actions/runs/23513343286
(they pass locally, but for some reason one of the tests had fewer waters.. so testing on aws CI to make sure it matches).

IAlibay · 2026-03-25T15:36:41Z

Took a while, but cpuvslow tests also pass on CI: https://github.com/OpenFreeEnergy/pontibus/actions/runs/23536584339/job/68513643017

IAlibay · 2026-03-25T15:37:21Z

Merging since we have now achieved all key objectives of this PR. Validation on test systems will come after.

IAlibay and others added 7 commits January 19, 2026 21:18

Add various CI runners

51418ff

Add cpu vslow runner

99c310b

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7af3b9d

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update dev env

36d56c2

update ci for testing against deps main branches

fd1694f

First attempt at updating for openfe v1.9

0c874f9

unpin openfe

fd1cda0

[pre-commit.ci] auto fixes from pre-commit.com hooks

47ed129

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IAlibay added 4 commits March 7, 2026 16:52

add more tokenization tests for asfe

a5e8c30

deal with duplicates

eb1b4f0

Some fixes

fbd56ab

Various fixes

309f59d

pre-commit-ci Bot and others added 5 commits March 8, 2026 08:41

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rename setup unit for ASFE

3b0921b

Rename tests

8d41c5d

Update tests

aeacb78

Fix up tests

546123f

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IAlibay added 2 commits March 8, 2026 20:27

Add news item

4f2ac4f

update API docs

9d6b77c

IAlibay marked this pull request as ready for review March 10, 2026 07:27

j-wags self-assigned this Mar 17, 2026

jameseastwood mentioned this pull request Mar 17, 2026

Add extra runners for latest deps & slow | gpu tests #177

Closed

Merge branch 'update-v1.9' of github.com:OpenFreeEnergy/pontibus into…

1d30380

… update-ci

j-wags approved these changes Mar 17, 2026

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IAlibay added 2 commits March 17, 2026 18:44

Add documentation to test classes for clarity

6925f09

Added docstring to test classes explaining protocol results generation and simulation duration.

Add docstring for protocol result tests

e9e9014

Added docstring to clarify protocol result generation and simulation expectations.

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j-wags approved these changes Mar 19, 2026

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atravitz and others added 4 commits March 24, 2026 08:21

add openff deps from main

0d813c9

Merge pull request #178 from OpenFreeEnergy/update-ci

befc3ed

Add runners for main branch deps

Merge branch 'main' of github.com:OpenFreeEnergy/pontibus into update…

2921e9b

…-v1.9

Add PR also to ci-dev-main

0ed059d

IAlibay commented Mar 24, 2026

View reviewed changes

IAlibay added 5 commits March 24, 2026 17:48

bump up checkout to v6

59bf03a

fix various typos

bffe417

Fix dev CI

201a02e

bump up openfe to 1.9+ in pixi.toml

ec9978b

change the message for it to work with 1.9 and 1.10

d31253e

IAlibay mentioned this pull request Mar 24, 2026

Should bleeding edge CI run on PRs #192

Closed

fix gpu test

89a695a

Add fix for slow tests

b3b3bd6

Merge branch 'main' into update-v1.9

2e00013

IAlibay merged commit b1877a0 into main Mar 25, 2026
11 of 13 checks passed

IAlibay deleted the update-v1.9 branch March 25, 2026 15:38

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