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[DNM] Refactor rmsd.py #75

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hannahbaumann wants to merge 82 commits into from
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[DNM] Refactor rmsd.py #75

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4b257b2
Fix stab at fixing multi chain RMSD analysis
hannahbaumann Dec 18, 2025
236ff72
Some updates
hannahbaumann Dec 18, 2025
d274b0c
Add tests
hannahbaumann Dec 18, 2025
f3634dd
Some fixes
hannahbaumann Dec 19, 2025
e92adb3
Add another test
hannahbaumann Dec 19, 2025
b528ca2
Move some tests to use skipped smaller data
hannahbaumann Jan 16, 2026
a477bc1
Test out zenodo dealings
hannahbaumann Jan 16, 2026
ad84082
Try to improbe speed
hannahbaumann Jan 16, 2026
8ba8087
Try removing locking
hannahbaumann Jan 16, 2026
ead7951
Run downloads before the testing to have a single download for all th…
hannahbaumann Jan 19, 2026
f898a35
add import pooch
hannahbaumann Jan 19, 2026
c675a5c
Test out more
hannahbaumann Jan 19, 2026
88e456d
Ensure datasets get closed
hannahbaumann Jan 19, 2026
73a8e4d
Move to per test download again
hannahbaumann Jan 19, 2026
43aaca2
Remove commented out lines
hannahbaumann Jan 21, 2026
c165525
Test out adding an extra slash
hannahbaumann Jan 21, 2026
5f17770
Switch to all version doi
hannahbaumann Jan 21, 2026
c28286e
Download url directly
hannahbaumann Jan 21, 2026
197b6ba
Small fix
hannahbaumann Jan 21, 2026
b45390a
Change url
hannahbaumann Jan 21, 2026
1d70936
Add missing s
hannahbaumann Jan 21, 2026
20084c3
Switch to api url
hannahbaumann Jan 21, 2026
1a1c916
Revert to old cli
hannahbaumann Jan 22, 2026
59c7392
Update cli.py
hannahbaumann Jan 22, 2026
5e135ab
Update cli.py
hannahbaumann Jan 22, 2026
a9a8780
Update tests for new results
hannahbaumann Jan 23, 2026
92af45b
Change shift to enable other boxes
hannahbaumann Jan 23, 2026
8ea3585
Update multichain code
hannahbaumann Jan 26, 2026
220d504
Add ligand in shifting
hannahbaumann Jan 26, 2026
8c44cb2
USe new shift class instead of old minimiser since that one is no lon…
hannahbaumann Jan 26, 2026
d13495f
Update some tests
hannahbaumann Jan 26, 2026
c34c97c
Update conftest
hannahbaumann Jan 26, 2026
0161673
Update to v2
hannahbaumann Jan 26, 2026
9b6ca69
Update tests
hannahbaumann Jan 26, 2026
1d5c849
Update rmsd test, currently large rmsd till rmsd fix comes in
hannahbaumann Jan 26, 2026
f4e88e2
Make last test pass
hannahbaumann Jan 26, 2026
bd0c8ee
Switch to zenodo fetch
hannahbaumann Jan 26, 2026
ba4c912
remove lines
hannahbaumann Jan 26, 2026
157c02f
Update tests with large errors multichain failure
hannahbaumann Jan 27, 2026
98ea023
Apply suggestion from @hannahbaumann
hannahbaumann Jan 28, 2026
c5b2d70
Reuse zenodo specification
hannahbaumann Jan 28, 2026
54576ab
reorder install
hannahbaumann Jan 28, 2026
3aa52a5
Small fix
hannahbaumann Jan 28, 2026
ff6991a
Remove flaky retries
hannahbaumann Jan 28, 2026
7a30f69
Small fix
hannahbaumann Jan 28, 2026
ac1fe7b
Merge in the fix flakyness PR and update tests
hannahbaumann Jan 28, 2026
67a0913
Add wrapping to get positions to be greater than 0
hannahbaumann Jan 29, 2026
e706b11
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 29, 2026
260d72c
Small fix
hannahbaumann Jan 29, 2026
5e7a037
fix
hannahbaumann Jan 29, 2026
4fac0a0
Use ligand selection string instead of resname
hannahbaumann Jan 29, 2026
c329ba9
Update test files
hannahbaumann Jan 30, 2026
b5cc7e0
Rename ligand_wander to ligand_COM_drift
hannahbaumann Jan 30, 2026
56b0e61
split out per state analysis into its own function
hannahbaumann Jan 30, 2026
6c1a6c5
Apply suggestion from @hannahbaumann
hannahbaumann Feb 2, 2026
f4637f4
Remove unnecessary make_whole
hannahbaumann Feb 2, 2026
e7d6935
Merge branch 'main' into fix_rmsd_multichain
hannahbaumann Feb 3, 2026
deb5126
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 3, 2026
fa3227e
Merge branch 'main' into fix_rmsd_multichain
hannahbaumann Feb 6, 2026
43eb039
Small fix
hannahbaumann Feb 6, 2026
73fe2ee
Merge branch 'main' into fix_rmsd_multichain
hannahbaumann Feb 6, 2026
6793f1d
Merge branch 'fix_rmsd_multichain' into rmsd_refactor
hannahbaumann Feb 10, 2026
7be4c53
Update tests
hannahbaumann Feb 10, 2026
68a2aab
Apply suggestion from @hannahbaumann
hannahbaumann Feb 10, 2026
198156b
Update src/openfe_analysis/transformations.py
hannahbaumann Feb 16, 2026
6f85466
Update src/openfe_analysis/transformations.py
hannahbaumann Feb 16, 2026
1d19473
Update src/openfe_analysis/transformations.py
hannahbaumann Feb 16, 2026
6cb52af
Update src/openfe_analysis/rmsd.py
hannahbaumann Feb 16, 2026
2ccc7a8
Update src/openfe_analysis/rmsd.py
hannahbaumann Feb 16, 2026
24163e5
Modify test for closest image shift
hannahbaumann Feb 16, 2026
5994774
Small fix
hannahbaumann Feb 16, 2026
b36a8e3
Merge branch 'fix_rmsd_multichain' into rmsd_refactor
hannahbaumann Feb 16, 2026
750543f
address review comments
hannahbaumann Feb 16, 2026
d2b2c34
Alternate ClosestImageShift
hannahbaumann Feb 16, 2026
592149c
Add caveat to doc string
hannahbaumann Feb 16, 2026
bb54931
Merge branch 'fix_rmsd_multichain' into rmsd_refactor
hannahbaumann Feb 16, 2026
61d3e46
Get ligands by fragment
hannahbaumann Feb 16, 2026
52792ac
Merge branch 'rmsd_refactor' of https://github.com/OpenFreeEnergy/ope…
hannahbaumann Feb 16, 2026
250dd9f
Small fix
hannahbaumann Feb 16, 2026
6544450
Merge branch 'main' into rmsd_refactor
hannahbaumann Feb 16, 2026
01e3d15
Merge branch 'main' into rmsd_refactor
hannahbaumann Feb 17, 2026
c529dd9
Merge branch 'main' into rmsd_refactor
hannahbaumann Feb 19, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ jobs:
~/.cache/openfe_analysis
# macOS cache location
~/Library/Caches/openfe_analysis
key: pooch-${{ matrix.os }}-v2
key: pooch-${{ matrix.os }}-v1

- name: "Download Zenodo data"
run: |
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