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Merged
lohedges merged 56 commits into from
Oct 8, 2025
Merged

Release 2025.2.0 #458

lohedges merged 56 commits into from
Oct 8, 2025

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@lohedges lohedges commented Oct 8, 2025 •
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This is the PR for the 2025.2.0 release of BioSimSpace.

  • 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 permission to release this code under the GPL3 license: [y]

lohedges added 30 commits July 1, 2025 15:43
@lohedges
Update Sire version. [ci skip]
1ed2d37
@lohedges
Typo. [ci skip]
f1dbcdf
@lohedges
Don't import Sire in setup.py. [closes #411]
50345d0
@lohedges
Merge pull request #412 from OpenBioSim/fix_411
30a7759 
Fix issue #411
@lohedges
Allow pre-processing to work with DataFrames of different length.
fb3943a 
[closes #414]
@lohedges
Merge pull request #415 from OpenBioSim/fix_414
0c8886a 
Fix issue #414
@lohedges
Make loguru dependency explicit. [closes #418]
a0db8e1
@lohedges
Merge pull request #419 from OpenBioSim/fix_418
15e1a7d 
Fix issue #418
@lohedges
Add support for the ABCG2 charge method.
0d3371f
@lohedges
Allow user to specify the template file. [ci skip]
7139cf6
@lohedges
Merge pull request #421 from OpenBioSim/feature_abcg2
7b3837a 
Add support for the ABCG2 charge method
@lohedges
Fix f-string formatting. [closes #422]
8e7117d
@lohedges
Offset lower and upper bound by start time. [closes #424]
5294708
@lohedges
Set the lower and upper bounds based on the start/end time. [ref #424]
c8aac52
@lohedges
Don't preprocess and updated expected MBAR and TI values.
04baad9
@lohedges
Use in-place import of ParmEd. [closes #426]
f45d37d
@lohedges
Don't require AnteChamber if NAGL is available. [closes #427]
736558b
@lohedges
Fix exception message.
ad72198
@lohedges
Fix Sandpit code. (Not sure why this was out-of-sync.)
9ea582b
@lohedges
Merge pull request #423 from OpenBioSim/fix_422. [ci skip]
e129fd1 
Fix issue #422
@lohedges
Merge pull request #425 from OpenBioSim/fix_424. [ci skip]
89c3c07 
Fix issue #424
@lohedges
Merge pull request #428 from OpenBioSim/fix_426_427
e51a855 
Fix issues #426 and #427
@lohedges
Expose OPC water function to docs. [ci skip]
e962c04
@lohedges
Merge pull request #431 from OpenBioSim/fix_430
915ac90 
Fix issue #430
@lohedges
Remove Python pin in install instructions. [ci skip]
0e16403
@lohedges
Merge pull request #432 from OpenBioSim/fix_install_instructions
d280272 
Remove Python pin in install instructions
@lohedges
Use array.tolist() rather than list(array). [closes #434]
9da8bce
@lohedges
Add custom __str__ method for each ATM protocol.
a5d889a
@lohedges
Fixed missing list conversion updates.
93137f4
@lohedges
Merge pull request #435 from OpenBioSim/fix_434
3653912 
Fix issue #434
@lohedges
Add chain identifier section.
4550870
@lohedges
Formatting tweak.
d8584c5
@lohedges
Allow renumbering of molecules when copying a system.
bc9610f
@lohedges
Fix typos.
3625f97
@lohedges
Reorder and add angle editing section for completeness.
8500bb3
@lohedges
Fixed formatting error.
7c3af5a
@lohedges
Merge pull request #440 from OpenBioSim/feature_system_renumber
d7c5ae4 
Add support for renumbering molecules when copying a system
@lohedges
Add note regarding cut-group definition. [ci skip]
3495298
@lohedges
Add note regarding use of private _sire_object attribute. [ci skip]
58ae8a4
@lohedges
Formatting tweak. [ci skip]
c45c574
@lohedges
Merge pull request #447 from OpenBioSim/feature_editing
3c3285f 
Add molecular editing tutorial. [ci skip]
@lohedges
Switch to 'dummy_modifications' rather than 'no_dummy_modifications'.
ce979ad
@lohedges
Merge pull request #450 from OpenBioSim/fix_dummy_modifications
39337f6 
Switch to positive boolean dummy_modifications default
@lohedges
Store element symbol in set, not object instance. [closes #453]
0db824a
@lohedges
Merge pull request #454 from OpenBioSim/fix_453
1a109a4 
Fix issue #453
@lohedges
Fix trajectory handling for perturbable reference systems.
3ddb093
@lohedges
Add unit test for perturbable trajectory reconstruction.
a2d9c55
@lohedges
Merge pull request #456 from OpenBioSim/fix_445
7009efa 
Fix issue #445
@lohedges
Merge branch 'main' into release_2025.2.0
7f5cd3e
@lohedges
Update Sire version.
30ca43b
@lohedges
Sync Sire version in Recursion CI.
9403a61
@lohedges
Update CHANGELOG for the 2025.2.0 release.
7d2c26c
@lohedges
Update Sire development requirement.
005123e
@lohedges lohedges temporarily deployed to biosimspace-build October 8, 2025 08:37 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build October 8, 2025 08:37 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build October 8, 2025 08:37 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build October 8, 2025 08:37 — with GitHub Actions Inactive
@lohedges lohedges merged commit 35ecb30 into main Oct 8, 2025
4 of 5 checks passed
@lohedges lohedges deleted the release_2025.2.0 branch October 8, 2025 10:00
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@lohedges