Support pymbar 4 #1173

mikemhenry · 2023-03-27T23:59:07Z

Description

Motivation and context

Resolves #???

How has this been tested?

Change log

Added support for pymbar 4 (pymbar 3 is also still supported)

mikemhenry · 2023-03-27T23:59:28Z

I will re-run this with pymbar 4 to make sure it still works

codecov · 2023-03-28T00:21:02Z

Codecov Report

Merging #1173 (1b3f9bd) into 0.10.x (a46516c) will decrease coverage by 2.67%.
The diff coverage is 37.93%.

ijpulidos · 2023-03-28T15:29:34Z

This is looking great, this is the way we should be using pymbar in perses, just through openmmtools. Let me know when you run the tests for pymbar 4 and I'll make the review.

mikemhenry · 2023-04-03T18:11:38Z

Pretty sure that the tests we expect to pass are, and the ones we expect to fail are

mikemhenry · 2023-04-03T18:11:49Z

So ready for review @ijpulidos

ijpulidos

As far as I can tell, there is still one place where we want to change the import

perses/perses/tests/test_repex.py

Line 3 in 648ad3e

import pymbar

After changing that it seems that this should be ready to go.

mikemhenry · 2023-07-18T21:45:27Z

@ijpulidos good catch! ready for re-review

ijpulidos

We need to change test_repex.py back to how it was, sorry!

ijpulidos · 2023-07-18T22:10:44Z

perses/tests/test_repex.py

@@ -416,7 +416,7 @@ def test_RESTCapableHybridTopologyFactory_repex_charge_transformation():
                # Extract uncorrelated energy matrix (u_ln) and samples from states (N_l)
                energy_matrix, samples_per_state = analyzer._compute_mbar_decorrelated_energies()
                # Compute free energies with boostrapping using pymbar
-                mbar = pymbar.MBAR(energy_matrix, samples_per_state, nbootstraps=200)
+                mbar = _pymbar_bar(energy_matrix, samples_per_state, nbootstraps=200)


Wait, this is MBAR, I think you had it right from the beginning, this hasn't change in pymbar 4 so we should be using it as we had it before without problems! Apologies for the confusion,

ijpulidos

I think we need to remove pip install of openmmtools

ijpulidos · 2023-07-19T15:57:51Z

devtools/conda-envs/test_env.yaml

+  - pip:
+    - git+https://github.com/choderalab/openmmtools.git


I don't think we need to install openmmtools from pip anymore, do we? Latest openmmtools release should have what we need.

I guess this was something temporary at the time.

Yes good catch!

devtools/conda-envs/test_env.yaml

ijpulidos

LGTM!

* run CI on new 0.10.x branch (#1212) * run CI on new 0.10.x branch * Update .github/workflows/CI.yaml Co-authored-by: Iván Pulido <[email protected]> --------- Co-authored-by: Iván Pulido <[email protected]> * print perses version on startup (#1176) * Update comments in `RESTCapableHybridTopologyFactory` (#1189) * update comments * bump ci --------- Co-authored-by: Iván Pulido <[email protected]> Co-authored-by: Mike Henry <[email protected]> * use python executable from env (#1174) * use python executable from env * run tests using the shell * parmed 4 seems to be giving us some issues * actually I think we want the newer parmed * pin pymbar for now * ooof, parmed != pymbar * add some more debugging to figure out how we are getting old parmed * Update devtools/conda-envs/test_env.yaml * see if shell=True fixes it * removed parmed by mistake * Support pymbar 4 (#1173) * switch to using pymbar 3 & 4 support from openmmtools * fix typo on import * fix yaml * switch to using pymbar 4 * missed a pymbar import * missed another one * bump ci * missed a import * go back to how it was * Update devtools/conda-envs/test_env.yaml --------- Co-authored-by: Iván Pulido <[email protected]> * Remove example testing (#1214) * Store initial and final topologies for all phases -- small molecule pipeline (#1210) * Initial and final topologies serialized per phase. * Using properties instead of private attrs. * Fix test * Remove uneeded code/attributes * bump ci * Store phase topologies separately * Fix tests. vacuum topologies expected. * Better docstring. --------- Co-authored-by: Mike Henry <[email protected]> * Improve docker building (#1200) * Added note about example for adding oe license * make docker file much simpler * build images in CI * forgot to add conda-forge * fix permissions on a step * get oe_license file mounted in docker container * mount path must be absolute * setup singulairty to test + fix testing on docker image * add some testing deps to the image * add -v for tests, fix envar * tests are failing, want to test rest of pipeline * use latest openmm version * hardcode perses version for now * bump ci * make sure we can make openeye dir * support a dev build as well * don't hardcode value * fix name clash * forgot to add conda-forge * bump ci * test docker image and fix missing deps * install ps * also push latest tag * don't build on tag since the conda-forge package won't exist yet * don't test the examples * Remove docker deb build, we can do these ourselves * better document container use * build a latest version for apptainer * build with 11.2 to make things more compatable * skip docker test to see if other bits build okay * see if I can get the step to fail if there is an error * skip docker tests to make sure apptainer builds okay * Add mpiplus and mpi4py to docker image * give correct path to oe license * add mpi stuff to docker * clean up diskspace before build * skip tests for singularity now that the only failures come from a package bug * Clean examples -- CLI protein-ligand example for Tyk2 (#1223) * Improving examples dir structure and readme * Adding Tyk2 CLI example * removing new-cli/ripk2 example (deprecated) * fix typo for link * Clarify tyk2 cli example docs * Realtime analysis interval to default to checkpoint interval (#1227) * CI miscellaneous fixes (#1217) * CI minor fixes. Allow codecov to fail. * bump ci --------- Co-authored-by: Mike Henry <[email protected]> * Changing offline freq default to checkpoint interval * Fixing input yaml for example * commenting offline-freq param --------- Co-authored-by: Mike Henry <[email protected]> * MPI example with dipeptide mutation (#1228) * peptide mutation MPI example added * better documentation of motivation * Fix/issue 1194 (#1230) * set cutoff distance in sterics_custom_nonbonded_force * matching cutoff for custom forces. Improving logic. * test for HTF nonbonded cutoff --------- Co-authored-by: Iván Pulido <[email protected]> * Fix/issue 1196 (#1229) * CI miscellaneous fixes (#1217) * CI minor fixes. Allow codecov to fail. * bump ci --------- Co-authored-by: Mike Henry <[email protected]> * added dels to contexts * Update perses/app/setup_relative_calculation.py --------- Co-authored-by: Iván Pulido <[email protected]> * Fix spectator support (#1233) * fix spectator support. Enabling test. * Test to run on GPU CI. * pin <4 for pymbar on GPU --------- Co-authored-by: Iván Pulido <[email protected]> Co-authored-by: Ivy Zhang <[email protected]>

mikemhenry added 2 commits March 27, 2023 15:03

switch to using pymbar 3 & 4 support from openmmtools

1b53329

fix typo on import

46b6edb

fix yaml

5716e35

mikemhenry added this to the 0.10.2 Bugfix release milestone Mar 28, 2023

mikemhenry added 4 commits March 31, 2023 14:53

switch to using pymbar 4

b341556

missed a pymbar import

e09d298

missed another one

996704a

Merge branch 'main' into feat/support_pymbar_4

c36247c

mikemhenry requested a review from ijpulidos April 3, 2023 18:11

mikemhenry added 2 commits April 25, 2023 09:49

Merge branch 'main' into feat/support_pymbar_4

0ebbd7b

Merge branch 'main' into feat/support_pymbar_4

4de5219

ijpulidos modified the milestones: 0.10.2 Bugfix release, 0.10.3 - Bugfix release May 8, 2023

mikemhenry changed the base branch from main to 0.10.x July 11, 2023 21:08

mikemhenry and others added 3 commits July 11, 2023 14:09

bump ci

31b5d73

Merge remote-tracking branch 'origin/0.10.x' into feat/support_pymbar_4

63d6c78

Merge branch '0.10.x' into feat/support_pymbar_4

648ad3e

ijpulidos reviewed Jul 18, 2023

View reviewed changes

missed a import

775057f

mikemhenry requested a review from ijpulidos July 18, 2023 21:45

Merge branch '0.10.x' into feat/support_pymbar_4

c5b86a0

ijpulidos reviewed Jul 18, 2023

View reviewed changes

mikemhenry added 2 commits July 18, 2023 15:25

go back to how it was

1f3b094

Merge branch '0.10.x' into feat/support_pymbar_4

40bc02a

mikemhenry enabled auto-merge July 18, 2023 22:26

mikemhenry requested a review from ijpulidos July 19, 2023 03:12

ijpulidos requested changes Jul 19, 2023

View reviewed changes

mikemhenry commented Jul 19, 2023

View reviewed changes

devtools/conda-envs/test_env.yaml Outdated Show resolved Hide resolved

Update devtools/conda-envs/test_env.yaml

1b3f9bd

mikemhenry requested a review from ijpulidos July 19, 2023 20:45

ijpulidos approved these changes Jul 19, 2023

View reviewed changes

mikemhenry added this pull request to the merge queue Jul 19, 2023

Merged via the queue into 0.10.x with commit 2d19c20 Jul 19, 2023

mikemhenry deleted the feat/support_pymbar_4 branch July 19, 2023 21:19

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Support pymbar 4 #1173

Support pymbar 4 #1173

mikemhenry commented Mar 27, 2023

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		- pip:
		- git+https://github.com/choderalab/openmmtools.git

Support pymbar 4 #1173

Support pymbar 4 #1173

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mikemhenry commented Mar 27, 2023

Description

Motivation and context

How has this been tested?

Change log

mikemhenry commented Mar 27, 2023

codecov bot commented Mar 28, 2023 • edited Loading

Codecov Report

ijpulidos commented Mar 28, 2023

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