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Release 2024.1.0 #278

Merged
merged 154 commits into from
Apr 15, 2024
Merged

Release 2024.1.0 #278

merged 154 commits into from
Apr 15, 2024

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lohedges
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This is the PR for the 2024.1.0 release of BioSimSpace.

Checklist

  • 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 December 16, 2023 21:46
@lohedges
Update Sire version. [ci skip]
4817660
@xiki-tempula
Merge remote-tracking branch 'upstream/main' into feat_2023.5.1
2571188
@xiki-tempula
Merge pull request #33 from Exscientia/feat_2023.5.1
0d03787 
Sync with 2023.5.1
@lohedges
Fix path to links file. [closes #231]
dc348b1
@lohedges
Fix redirection of stderr for logger. [ref #232]
e0b4007
@lohedges
Merge branch 'fix_231' into fix_232
224428d
@lohedges
Update copyright range.
c518ffe
@lohedges
Match atoms by coordinates.
3d3b197
@lohedges
Merge pull request #233 from OpenBioSim/fix_232
15e37d9 
Fix issues 231 and 232
@lohedges
Merge branch 'devel' into feature_atomcoordmatcher
90b6e9d
@lohedges
Merge pull request #235 from OpenBioSim/feature_atomcoordmatcher
dff31eb 
Update makeCompatibleWith to use the new AtomCoordMatcher
@lohedges
Add _generate_binary_run_file staticmethod.
90855ee
@lohedges
Allow use of a separate file as a reference for position restraints.
ddc5785
@lohedges
Run pytest-black against Python 3.11.
62763b6
@lohedges
Forgot to use selector for running pytest-black.
d18da44
@lohedges
Also need to add source files to selector.
4998dd2
@lohedges
Pin to pytest 7 until pytest-black is updated.
4175229
@lohedges
Call staticmethod on class, not instance.
b7944d1
@lohedges
Merge pull request #237 from OpenBioSim/fix_236
286a467 
Fix issue #236
@lohedges
Build Python 3.10 for macOS.
6ad3ac1
@lohedges
Update support range. [ci skip]
bec58fb
@lohedges
Remove redundant parmed import and references to parmed files.
5cc7dea 
[closes #242]
@lohedges
Expose FreeEnergyMixin protocols. [closes #243]
1730723
@lohedges
Remove shared properties when loading perturbable systems.
1cfa0bd 
[closes #241]
@lohedges
Merge pull request #244 from OpenBioSim/fix_241-243
d94c19b 
Fix issues #241, #242, and #243
@lohedges
Add support for using a reference system for position restraints.
7ab5c8d
@lohedges
Add support for FEP with AMBER molecular dynamics engine.
5dc399a
@lohedges
Fix funnel range used in correction calculation. [closes #246]
c8eba8d
@lohedges
Change file extensions for interchange files to Sire defaults.
c2aaf0b 
[closes #240]
@lohedges
Recover missing molecule0 and molecule1 properties. [closes #248]
50b5bb6
lohedges added 22 commits April 12, 2024 12:54
@lohedges
Use NAMD specific system in tests so we validate parsing too.
861f5d3
@lohedges
Make fixtures module specific.
b36da43
@lohedges
Add tests for steered MD and funnel metadynamics.
631f1a4
@lohedges
Revert copilot update to interchange file extensions.
4dcf175
@lohedges
Revert another copilot typo.
2c0b1e6
@lohedges
Merge pull request #272 from OpenBioSim/feature_amber_fep
fdff786 
Add support for AMBER as a free-energy perturbation engine.
[ci skip]
@lohedges
Merge branch 'devel' into final_fixes
23a3596
@lohedges
Only run funnel metadynamics test locally.
5bd3545
@lohedges
Port fileformat fix to sandpit.
1f7a46b
@lohedges
Update test description.
c1cb363
@lohedges
Merge remote-tracking branch 'exscientia/devel' into sync_exscientia
dac5521
@lohedges
Fix duplicate tests and add missing guards.
a1ec8af
@lohedges
Remove references to redundant "future" branch. [ci skip]
d8d5740
@lohedges
Remove references to mamba since libmamba is now default solver.
cfb4284 
[ci skip]
@lohedges
Merge branch 'final_fixes' into sync_exscientia
77d6cfa
@lohedges
Synchronise files untouched by Exs with core.
fc3897d
@lohedges
Add missing skipif decorator.
958eaf6
@lohedges
Guard test against missing GROMACS package.
d79961e
@lohedges
Merge pull request #277 from OpenBioSim/sync_exscientia
3abcec4 
Sync with Exscientia remote
@lohedges
Merge branch 'main' into release_2024.1.0
cd2547b
@lohedges
Update CHANGELONG for the 2024.1.0 release.
b7f68ba
@lohedges
Update Sire version.
769ff19
@lohedges lohedges temporarily deployed to biosimspace-build April 15, 2024 12:21 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build April 15, 2024 12:21 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build April 15, 2024 12:21 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build April 15, 2024 12:21 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build April 15, 2024 12:21 — with GitHub Actions Inactive
@lohedges lohedges merged commit 791bbd4 into main Apr 15, 2024
@lohedges lohedges deleted the release_2024.1.0 branch April 15, 2024 13:17
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4 participants
@lohedges @xiki-tempula @fjclark @msuruzhon