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Release 2024.3.0 #246

Merged
merged 527 commits into from
Oct 22, 2024
Merged

Release 2024.3.0 #246

merged 527 commits into from
Oct 22, 2024

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lohedges
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This is the PR for the 2024.3.0 release. I have created a branch from the tip of devel then back merged main into it (using ours) to combine the histories, as is done for BioSimSpace. I've also tweaked the CHANGELOG to add a bit more detail.

  • I confirm that I have merged the latest version of main into this branch before issuing this pull request (e.g. by running git pull origin main): [y]
  • I confirm that I have added a test for any new functionality in this pull request: [y]
  • I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [y]
  • I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
  • I confirm that I have permission to release this code under the GPL3 license: [y]

Suggested reviewers:

@chryswoods

lohedges and others added 30 commits April 22, 2024 11:20
@lohedges
Add get_force monkey-patch to get OpenMM force from EMLEEngine.
e5bba90
@lohedges
Add support for using OpenMM-ML lambda_emle global parameter.
7fb96b6
@lohedges
Allow decoupling of electrostatics from ML potential.
fcdc2fe
@lohedges
Add QMForce first so position is guaranteed.
506d234
@lohedges
Add a null CustomBondForce to enable lambda_emle global parameter.
4ec9b78
@lohedges
Clamp the lambda value to between 0 and 1.
37fe9d8
@lohedges
Improve docstring.
56ac6c6
@lohedges
Improve docstring for get_forces and return forces as a tuple.
e5c97ad
@lohedges
Add unit test for use of EMLEForce with OpenMM-ML.
999f206
@lohedges
Add maximumCutoff method to TriclinicBox class. [closes #189]
5cdda56
@lohedges
Typos.
3894035
@chryswoods
Merge pull request #190 from OpenBioSim/fix_189
cb69318 
Fix issue #189
@chryswoods
Merge branch 'devel' into feature_trajectory_cache
6dc15cd
@lohedges
Add section about using an EMLEForce with OpenMM-ML.
ef5225d
@chryswoods
Merge pull request #188 from OpenBioSim/feature_trajectory_cache
8cff51b 
Feature trajectory cache
@lohedges
Added alanine-dipeptide conformational sampling tutorial.
56489a4
@lohedges
Save topology and coordinate file in same function call.
08bfad3
@lohedges
Add section on diels-alder reaction.
62f5d22
@lohedges
Typos and formatting tweaks.
91413a2
@lohedges
Add note that OpenMM-ML isn't installed by default.
dd0e75a
@lohedges
Use CPU platform for tutorial.
4732fc6
@lohedges
Formatting tweak.
4c2d8a1
@lohedges
Remove redundant note.
38eed22
@lohedges
Typos.
a89be39
@lohedges
Add introduction sire-emle notebook.
360db61
@lohedges
Use comparable settings.
e52e10a
@lohedges
QM region is the substrate, not enzyme.
b71b1e7
@lohedges
Clean example notebook.
343fdb9
@lohedges
Add option to redistribute excess QM charge.
b05c9e7
@lohedges
Formatting tweak.
99eb489
@lohedges
Update callback to take optional list of MM atom indices.
6b57a66
@lohedges
Clarify that link atoms & virtual charges are at end of lists. [ci skip]
852e37a
@lohedges
Update callback signature in tests.
d4e8c2d
@lohedges
Use ethane~methanol perturbation and reference platform.
c58fc13
@lohedges
Use preserveState=True rather than saving state ourselves.
152ab02
@lohedges
Only run constraint check on Linux.
dcc7164
@lohedges
Give custom OpenMM forces meaningful names.
26b5008
@lohedges
Use named restraint forces.
718d573
@lohedges
Correct molecule index. [ci skip]
34df271
@lohedges
Remove redundant notes. [ci skip]
c23b78a
@lohedges
Typo. [ci skip]
223f90c
@lohedges
Return clone of molecules. [ref #218]
4cd098e
@lohedges
Add method to return underlying context from dynamics object. [ci skip]
41b381f
@lohedges
Merge pull request #243 from OpenBioSim/feature_emle
4d94050 
Add support for QM/MM
@lohedges
Don't udpate constraints when computing energy trajectory.
2dc4c6e
@lohedges
Merge branch 'main' into release_2024.3.0
be7384c
@lohedges
Update CHANGELOG for the 2024.3.0 release.
8a2f67c
@lohedges
Re-add Python 3.12 CI exclusions for macOS.
b52e4bf
@fjclark
Improve annihilate docstring [ci skip]
cd33b56 
Make it clear that annihilate removes intramolecular bonded
interactions, not just intramolecular nonbonded interactions,
as might be expected from some of the ABFE literature.
@chryswoods
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Excellent - thanks for doing this

@lohedges lohedges merged commit 9a2d331 into main Oct 22, 2024
@lohedges lohedges deleted the release_2024.3.0 branch October 22, 2024 11:59
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@chryswoods chryswoods Awaiting requested review from chryswoods

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@lohedges @chryswoods @jmichel80 @JMorado @nigel-palmer-cresset @mb2055 @fjclark