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Release 2024.4.0 #282

Merged
merged 124 commits into from
Feb 5, 2025
Merged

Release 2024.4.0 #282

merged 124 commits into from
Feb 5, 2025

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lohedges
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@lohedges lohedges commented Feb 4, 2025

This is the PR for the 2024.4.0 release of Sire.

  • 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]

akalpokas and others added 30 commits July 10, 2024 11:14
@akalpokas
Initial update for angle restraints
05e38a9
@akalpokas
Intial addition of alchemical dihedral restraints and angle restraint…
12af94a 
…s update
@akalpokas
Update wrappers for angle and dihedral restraints classes
8809ac5
@akalpokas
Added intial python code for implementing alchemical dihedral restraints
386912d
@akalpokas
Added prototype code for adding alchemical dihedral restraints to Ope…
69a7ee2 
…nMM system
@akalpokas
Fix conversion of dihedral restraints to OpenMM system
c29c4eb
@akalpokas
Added full end-to-end alchemical dihedral restraints implementation -…
4a0726d 
… bugs might still be lurking somewhere
@akalpokas
Added full end-to-end alchemical angle restraints implementation, and…
9eeb824 
… also renamed the core alchemical angle/dihedral restraint c++ files
@akalpokas
Add the missing corelib files for angle restraints
a500bc9
@akalpokas
Merge branch 'OpenBioSim:devel' into feature_alchemical_restraints_contd
55eb13e
@lohedges
Update to the 2024.4.0.dev release. [ci skip]
ff207f5
@lohedges
Fix note formatting. [ci skip]
bee9b06
@lohedges
Fix tutorial section formatting. [ci skip]
4fcc147
@lohedges
Fix instantiation of QByteArray and counting of bytes. [closes #249]
926f082
@lohedges
Increase wait before terminating QThreads. [closes #251] [ci skip]
a2370a4
@lohedges
Update CHANGELOG. [ci skip]
808dad7
@lohedges
Give thread a chance to finish and inform user. [ci skip]
9d9f51b
@lohedges
Merge pull request #250 from OpenBioSim/fix_249
146632e 
Fix issue #249
@lohedges
Expose missing timeout kwarg in dynamics.minimise(). [closes #253]
a5d704f
@lohedges
Add include_constrained_energies kwarg to map. [ref #255]
32f27a4
@lohedges
Add consistent minimisation settings. [closes #255]
53182c3
@lohedges
Update CHANGELOG.
b7cee4b
@lohedges
Merge pull request #254 from OpenBioSim/fix_253
97d7f2f 
Fix issue #253
@fjclark
Make Boresch restraints correction consistent with F=2kx
be8aa3a 
Previously, the correction was implemented assuming F=kx. This lead
to erroneously favourable absolute free energies of binding by
1.23 kcal mol-1.
@fjclark
Update docs to make clear that F = 2kx for restraints
63e76ea 
Update the restraint function docstrings, restraints tutorial,
and changelog.
@lohedges
Don't always save frames and energies after dynamics.run() [ref #256]
add86c0
@lohedges
Simplify test logic.
175ecf4
@lohedges
Fix thread safety issue in OpenMM minimiser. [closes #259]
46b5d3f
@lohedges
Remove redundant include.
627926e
@lohedges
Update CHANGELOG.
a291ea4
lohedges and others added 15 commits January 21, 2025 16:30
@lohedges
Merge pull request #273 from OpenBioSim/feature_repex
2cd0d82 
Add support for replica exchange and REST2
@lohedges
Exclude alchemical ions from the REST2 region.
5dbc955
@lohedges
Allow user to compute energies over subset of lambda windows. [ci skip]
af71419
@lohedges
Compute num_lambda_windows when lambda_windows is not None. [ci skip]
ff8b4fc
@lohedges
Clarify that all windows are used when None. [ci skip]
790f7d2
@lohedges
Merge pull request #277 from OpenBioSim/fix_rest2_alchemical_ions
961e15e 
Exclude alchemical ions from the REST2 region
@fjclark
Fix hasForceSpecificEquation
fc30fb2 
This now returns true if there is a default equation for the force.
@fjclark
Update changelog [ci skip]
5c2dacf
@fjclark
Merge branch 'devel' into bugfix-force-specific-equation [ci skip]
3cbe190
@lohedges
Merge pull request #280 from fjclark/bugfix-force-specific-equation
b3a566b 
Fix hasForceSpecificEquation
@lohedges
Add support for OpenMM MonteCarloMembraneBarostat.
b29e168
@lohedges
Merge pull request #281 from OpenBioSim/feature_membrane_barostat
a5278e9 
Add support for OpenMM MonteCarloMembraneBarostat
@lohedges
Merge branch 'main' into release_2024.4.0
68b2ad8
@lohedges
Update CHANGELOG for the 2024.4.0 release.
8e8582b
@lohedges
Bump version.
4199df4
@lohedges lohedges merged commit 14bcc19 into main Feb 5, 2025
4 of 5 checks passed
@lohedges lohedges deleted the release_2024.4.0 branch February 5, 2025 08:35
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4 participants
@lohedges @akalpokas @fjclark @mb2055