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Merged
lohedges merged 37 commits into from
Nov 10, 2025
Merged

Release 2025.3.0 #469

lohedges merged 37 commits into from
Nov 10, 2025

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@lohedges lohedges commented Nov 10, 2025

This is the PR for the 2025.3.0 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 added 30 commits October 8, 2025 11:52
@lohedges
Remove survey section.
a4c16fd
@lohedges
Update Sire development requirement. [ci skip]
20ad1b8
@lohedges
Fix incorrect conditional.
aec0bfd
@lohedges
Merge pull request #460 from OpenBioSim/fix_459
1096b37 
Fix issue #459
@lohedges
Wrap sire.legacy.IO.setCoordinates and sr.io.get_coords_array.
cc74635
@lohedges
Fix incorrect context manager name.
15f9267
@lohedges
Fix typo in RDKit d2d option. [closes #449] [ci skip]
527321f
@lohedges
Use absolute path for node directory. [ci skip]
d62076a
@lohedges
Merge pull request #463 from OpenBioSim/fix_462
2cc1724 
Fix issue #462
@lohedges
Add unit test for setCoordinates functionality.
0412cd4
@lohedges
Merge branch 'devel' into feature_set_coordinates
7f8a2d3
@lohedges
Grammar tweak.
5db2bc8
@lohedges
Fix typo.
099db38
@lohedges
Merge pull request #465 from OpenBioSim/feature_set_coordinates
0850575 
Add support for setting coordinates of all atoms from a NumPy array
@lohedges
Switch to new Sire API.
010ccb3
@lohedges
Refactor imports.
5be5f78
@lohedges
Add lazy_import to requirements.
0e951c4
@lohedges
Fix importing of Sandpit in isolation.
5cb0763
@lohedges
Fix incorrect conversion of BioSimSpace API call.
624b3ca
@lohedges
Handle new Sire API already being activated.
6850eaa
@lohedges
Use verbose errors for testing.
d1ad043
@lohedges
Fix missing Sire API updates and lazy load issues.
39e8180
@lohedges
More Sire API conversion fixes.
cc9b6af
@lohedges
Fix docstring placement. [ci skip]
f7f86bf
@lohedges
Fix tutorialUrl call. [ci skip]
c8106a1
@lohedges
Don't lazy import modules in a Jupyter notebook.
d36f94a
@lohedges
Fix missing Sire API conversion.
32e2f05
@lohedges
Allow disabling of lazy import via environment variable. [ci skip]
590a0c2
@lohedges
Switch tutorial to new Sire API. [ci skip]
2ed14cc
@lohedges
Need to import internal modules too.
4c88f30
@lohedges lohedges temporarily deployed to biosimspace-build November 10, 2025 13:19 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build November 10, 2025 13:19 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build November 10, 2025 13:19 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build November 10, 2025 13:19 — with GitHub Actions Inactive
@lohedges lohedges merged commit 93ee89c into main Nov 10, 2025
4 of 5 checks passed
@lohedges lohedges deleted the release_2025.3.0 branch November 10, 2025 13:50
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@lohedges