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Release 2025.1.0#410

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lohedges merged 50 commits intomainfrom
release_2025.1.0
Jul 1, 2025
Merged

Release 2025.1.0#410
lohedges merged 50 commits intomainfrom
release_2025.1.0

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@lohedges lohedges commented Jul 1, 2025

This is the PR for the 2025.1.0 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 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 February 5, 2025 15:37
@lohedges
Update Sire version.
c25b56b
@lohedges
Upgrade to Black 25.
c649536
@lohedges
Allow user to force stereo inference. [ref OpenBioSim/sire#287]
a24e3a8
@lohedges
Need to wrap boolean property map option.
a97cc19
@lohedges
Merge pull request #388 from OpenBioSim/fix_sire_287
b12baa4 
Allow user to force stereo inference
Update Exscientia Sandpit SOMD config settings
8a323fc 
Update settings to match those inn the main version of the code:
see 976ab36
@lohedges
Merge pull request #390 from fjclark/devel
de6629c 
Update Exscientia Sandpit SOMD config settings
@lohedges
Make formal charge calculation more robust. [closes #392]
5c05464
@lohedges
Always try both PDB and SDF format, i.e. only the order changes.
a8185e3
@lohedges
Blacken.
faee4ff
@lohedges
Add unit test for fallback for failed formal charge calculation.
5fec8d7
@lohedges
Merge pull request #393 from OpenBioSim/fix_392
974cdd1 
Fix issue #392
@lohedges
Add support for ff19SB.
f56b6bc
Fix for issue #397, also adds utility function to get name of node di…
b1cb6ba 
…rectory
@xiki-tempula @lohedges
Allow Gromacs Process to store density information (#7)
bba6729 
Add a new distance of cm
@xiki-tempula @lohedges
Hang killer (#8)
08e514b 
Implement a hang killer at BSS level
@lohedges
Allow pert file without modifications to dummy bonded terms.
d32e415
@lohedges
Remove AnteChamber check. No version is reported for AmberTools 24.
75e9549
@lohedges
Skip test until we can get version info or work out reason for failure.
de9db8a
@lohedges
Merge pull request #400 from OpenBioSim/sync_recursion2
8ba863f 
Sync with Recursion remote
@lohedges
Merge branch 'devel' into feature_no_ghost_mods
e2dcacf
Fix for is_lambda1 in Somd1 processes
41534e6
@lohedges
Add link to survey. [ci skip]
6c63b6d
@lohedges
Highlight survey. [ci skip]
9ed2d1f
Import proper errors in somd config
db03a53
@lohedges
Typo. [ci skip]
5d748ce
Amber config typo fix [ci skip]
44eeb7c
Fix for AMBER runs on perturbable systems with restraints
580c91b
Fix for previous commit - removes old file save [ci skip]
8fe807a
@lohedges
Return unsquashed system from getFrame(). [closes #402]
82877ed
lohedges added 20 commits June 12, 2025 11:06
@lohedges
Merge pull request #403 from OpenBioSim/fix_402
40c588c 
Fix issue #402
@lohedges
Move sandpit test file to the correct path. [ci skip]
baad606
@lohedges
Return full data frame, not just lambda array.
754d7f0
@lohedges
Parquet lambda_array metadata is no longer needed.
93fc038
@lohedges
Merge branch 'devel' into feature_ff19sb
5ce173b
@lohedges
Merge branch 'devel' into feature_no_ghost_mods
e4abd56
@lohedges
Test that we can parameterise with ff19SB, which includes CMAP terms.
2e5f4fa
@lohedges
Simplify finite difference calculation. [ci skip]
71145d4
@lohedges
Add support for OPC water model. [ci skip]
e657eab
@lohedges
Don't duplicate the defaults directive. [ci skip]
59b512f
@lohedges
Allow user to disable data preprocessing.
10187b3
@lohedges
Distinguish OPC and TIP4P water. [ci skip]
98b26d3
@lohedges
Merge remote-tracking branch 'origin/fix_397' into feature_ff19sb
e6af7ab
@lohedges
Allow node to be run in a specified working directory.
9ad668c
@lohedges
Merge branch 'feature_no_ghost_mods' into feature_ff19sb
eb9ff4a
@lohedges
Merge branch 'feature_focused_sampling' into feature_ff19sb
88b02bc
@lohedges
Handle different boolean property types.
5b0c565
@lohedges
Merge pull request #406 from OpenBioSim/feature_ff19sb
f9e890f 
Add support for ff19SB force field
@lohedges
Merge branch 'main' into release_2025.1.0
1050a69
@lohedges
Update CHANGELOG for the 2025.1.0 release.
bf3f5b0
@lohedges lohedges added the enhancement New feature or request label Jul 1, 2025
@lohedges lohedges temporarily deployed to biosimspace-build July 1, 2025 13:07 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build July 1, 2025 13:07 — with GitHub Actions Inactive
@lohedges lohedges had a problem deploying to biosimspace-build July 1, 2025 13:07 — with GitHub Actions Failure
@lohedges lohedges temporarily deployed to biosimspace-build July 1, 2025 13:07 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build July 1, 2025 13:07 — with GitHub Actions Inactive
@lohedges lohedges merged commit 0f3d159 into main Jul 1, 2025
4 of 5 checks passed
@lohedges lohedges deleted the release_2025.1.0 branch July 1, 2025 13:49
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