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Release 2025.4.0#501

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lohedges merged 89 commits intomainfrom
release_2025.4.0
Feb 17, 2026
Merged

Release 2025.4.0#501
lohedges merged 89 commits intomainfrom
release_2025.4.0

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@lohedges lohedges commented Feb 17, 2026

This is the PR for the 2025.4.0 release of BioSimSpace.

  • I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [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 permission to release this code under the GPL3 license: [y]

lohedges and others added 30 commits November 10, 2025 21:52
@lohedges
Update Sire development version.
1c1aded
Adds proper distances from COM restraints for both the bound and free…
7ea9f19 
… ligands
Merge branch 'devel' into fix_470
bce30a6
@lohedges
Add ReplicaSystem implementation for replica exchange simulations.
de2ff17
@lohedges
Handle squashed AMBER FEP trajectories.
62bc1c7
@lohedges
Add method to get all replicas as a list of System objects.
b6f7296
@lohedges
Add unit test for squashed representation handling.
d66853d
Remove splatting to fix python 3.10 compatibility issue
a901746
@lohedges
Merge pull request #471 from OpenBioSim/fix_470
ead4092 
Fix for ATM centre of mass restraints
@lohedges
Merge branch 'devel' into feature_replica_system
3b40fb2
@lohedges
Remove debugging flag.
581013b
@lohedges
Restore missing fixture.
dccf1ae
@lohedges
Merge pull request #473 from OpenBioSim/feature_replica_system
b1e255e 
Feature replica system
@lohedges
Fix lazy import issues.
d18b96b
@lohedges
Merge pull request #475 from OpenBioSim/fix_474
c1e961f 
Fix issue #474
@lohedges
Allow translation of custom coordinates property.
5391f2a
@lohedges
Merge pull request #477 from OpenBioSim/fix_translate
076eaac 
Allow translation of custom coordinates property
@lohedges
Update property name in map. [ci skip]
eb4931a
@lohedges
Merge pull request #479 from OpenBioSim/fix_translate
d618222 
Update property name in map
@lohedges
Make fixing of perturbable zero sigmas optional.
63fdb75
@lohedges
Merge pull request #482 from OpenBioSim/fix_ghost_sigmas
3364c2c 
Make zeroing of dummy atom LJ sigmas optional
@lohedges
Add missing kwarg to merge wrapper function.
1d064c0
@lohedges
Update GROMACS NPT config to match sandpit. [closes #484]
f4e9cd4
@lohedges
Correctly scale tau-p according to dt and nstpcouple.
e3add88
@lohedges
Merge pull request #485 from OpenBioSim/fix_484
cc56ae7 
Fix issue #484
@lohedges
Fix inconsistencies in merge code.
13d0fc0
@lohedges
Make sure not to connect zeroed bonds.
2d5043c
@lohedges
Merge pull request #488 from OpenBioSim/fix_merge_bugs
30d3b28 
Fix inconsistencies in merge code
@lohedges
Add missing comment. [ci skip]
aa0c8f7
@lohedges
Just set intrascale on the basis of the connectivity.
cda1866
@lohedges
Add pre-commit.
7dffae2
@lohedges
Add namd3 to allowed MD engines.
e73b73f
@lohedges
Remove black from test requirements.
20db0c1
@lohedges
Update gitignore.
0711b36
@lohedges
Add rattler-build to development environment.
d3790a2
@lohedges
Need to set PYTHONPATH for tests.
9c9c5e5
@lohedges
Use pixi install of rattler-build.
3103ac9
@lohedges
Add MANIFEST to make sure non-Python test files are included.
33fd75c
@lohedges
Make test script platform agnostic.
94d01b4
@lohedges
Skip tests if tLEaP is missing.
3cac249
@lohedges
Avoid file locking errors on Windows.
31acf21
@lohedges
Update docs regarding pre-commit and ruff. [ci skip]
efc6548
@lohedges
Merge pull request #500 from OpenBioSim/feature_rattler
44276a7 
Modernise build system
@lohedges
Remove redundant dependency.
89e19d5
@lohedges
Fix missing Sire pins.
02565fc
@lohedges
Add note about OpenCL activation.
e2bb0c5
@lohedges
Update OpenCL activation instructions. [ci skip]
5807cca
@lohedges
Update workflow scripts to support macOS Python 3.12 builds.
3d96354
@lohedges
Merge branch 'main' into release_2025.4.0
458ca23
@lohedges
Update CHANGELOG for the 2025.4.0 release.
e932ea1
@lohedges
Update Sire pins.
7ca3992
@lohedges
Update date.
0791b78
@lohedges lohedges added the enhancement New feature or request label Feb 17, 2026
@lohedges lohedges temporarily deployed to biosimspace-build February 17, 2026 08:20 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build February 17, 2026 08:20 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build February 17, 2026 08:20 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build February 17, 2026 08:20 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build February 17, 2026 08:20 — with GitHub Actions Inactive
@lohedges lohedges merged commit 5814ae7 into main Feb 17, 2026
5 checks passed
@lohedges lohedges deleted the release_2025.4.0 branch February 17, 2026 08:45
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