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Release 2026.1.0#525

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lohedges merged 61 commits into
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release_2026.1.0
Jun 29, 2026
Merged

Release 2026.1.0#525
lohedges merged 61 commits into
mainfrom
release_2026.1.0

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@lohedges

@lohedges lohedges commented Jun 29, 2026

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This is the PR for the 2026.1.0 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
Update Sire development version.
41dafbc
@lohedges
Fix ring-break/change detection logic by using paths only.
7ca8c75
@lohedges
Add unit tests for ring break and size change detection.
0d46769
@lohedges
Add missing test guards.
7ea22b1
@lohedges
Merge pull request #502 from OpenBioSim/fix_ring_break_detection
0a04a75 
Fix ring break detection
@lohedges
Update pre-commit. [ci skip]
fbf972a
@lohedges
Autoformat. [ci skip]
99cef0d
@lohedges
Added functionality for adding ions to a system.
a8f2515
@lohedges
Add ion_conc option to addIons and standardise with solvate.
9e22a86
@lohedges
Clarify ion_conc parameter for addIons function.
1e67e0b
@lohedges
Allow user to specify counterion.
3385d7f
@lohedges
Handle intrascale merging for GLYCAM molecules.
e2f0b9a
@lohedges
Optimisations for ring breaking / growing checks.
379e51a
@lohedges
Apply intrascale and ring break check optimisations to sandpit.
9c880ba
@lohedges
Duplicate parameterised merge test in sandpit.
47e6772
@lohedges
Merge pull request #506 from OpenBioSim/fix_glycam
5db39f1 
Fix GLYCAM force field merging
@lohedges
Add support for merging CMAP terms.
db81b4c
@lohedges
Merge pull request #508 from OpenBioSim/feature_perturbable_cmap
f6c9979 
Add support for merging CMAP terms
@lohedges
Handle normalised lambda and lambda_grad metadata entries.
c7ae572
@lohedges
Handle normalisation in a backwards compatible way.
337de4a
@lohedges
Normalise to floats for simplicity.
d107138
@lohedges
Merge pull request #510 from OpenBioSim/fix_lambda_grad_format
0130f10 
Handle normalised lambda and lambda_grad metadata entries
@lohedges
Add backwards compatible normalisation function.
0908b42
@lohedges
Restrict to energy trajectory parquet files.
74f60d4
@lohedges
Add regression test for ring-breaking intrascale fix.
b8ce6c9
@lohedges
Merge pull request #513 from OpenBioSim/fix_intrascale_merge
38ed3b3
@lohedges
Update mergeIntrascale function call.
5bc1561
@lohedges
Add ring-breaking intrascale connectivity regression test.
9e5b68f
@lohedges
Merge pull request #514 from OpenBioSim/fix_ring_break_merge
3b50ecc 
Fix ring break merge
@lohedges
Add missing test guards.
945cc85
lohedges and others added 22 commits May 12, 2026 16:12
@lohedges
Merge branch 'feature_add_ions' into feature_ring_break_softcore
f97ae7a
@lohedges
Merge pull request #518 from OpenBioSim/feature_ring_break_softcore
769a957
@lohedges
Filter pairs to remove ghost atoms.
9934335
@lohedges
Expose max_path and max_ring_size kwargs.
8e9c6ba
@lohedges
Merge pull request #520 from OpenBioSim/fix_519
329cf76
@lohedges
Try pinning to a recent openff-interchange-base.
7a3acf9
@lohedges
Use pre-parameterised inputs to avoid SQM issue.
f4804c0
@lohedges
Conditionally pin for Python 3.11+.
c0193ed
@lohedges
OpenFF requires setuptools for Python 3.10.
90a479e
@lohedges
Add guard.
dde861c
@lohedges
Pin setuptools to <82.
10e0835
@lohedges
Merge pull request #524 from OpenBioSim/fix_523
07765cb
@akalpokas
Add support for custom region of interest mapping in matchAtoms function
1853596
@akalpokas
Update protein mutation tutorial with a proline mutation case
4343bed
@akalpokas
Polish formatting within the rendered protein fep tutorial
77c4bc1
@akalpokas
blacken
d3dab96
@akalpokas
Add pytest guard to avoid running test_custom_roi_ring_break_merge if…
c56600d 
… test environment has no ambertools [ci skip]
@akalpokas
Address requested changes regarding custom_roi_mapping
6fe7759
@lohedges
Merge pull request #522 from akalpokas/feature_custom_ROI_maps
86174cb
@lohedges
Merge branch 'main' into release_2026.1.0
7e51432
@lohedges
Update Sire version.
f9c4bed
@lohedges
Update CHANGELOG.
5b7c748
@lohedges lohedges added the enhancement New feature or request label Jun 29, 2026
@lohedges lohedges temporarily deployed to biosimspace-build June 29, 2026 10:42 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 29, 2026 10:42 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 29, 2026 10:42 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 29, 2026 10:42 — with GitHub Actions Inactive
@lohedges lohedges had a problem deploying to biosimspace-build June 29, 2026 10:42 — with GitHub Actions Failure
@lohedges lohedges merged commit 6b9ae00 into main Jun 29, 2026
4 of 5 checks passed
@lohedges lohedges deleted the release_2026.1.0 branch June 29, 2026 11:34
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@lohedges @akalpokas